<?xml version="1.0" encoding="us-ascii"?><InstanceReport xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><Version>2.4.0.8</Version><ReportLongName>2113100 - Disclosure - Notes, Mortgage Notes and Obligations Payable</ReportLongName><DisplayLabelColumn>true</DisplayLabelColumn><ShowElementNames>false</ShowElementNames><RoundingOption /><HasEmbeddedReports>false</HasEmbeddedReports><Columns><Column FlagID="0"><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><CurrencyCode /><FootnoteIndexer /><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios><MCU><KeyName /><CurrencySymbol /><contextRef><ContextID>D2013Q2YTD</ContextID><EntitySchema>http://www.sec.gov/CIK</EntitySchema><EntityValue>0001216596</EntityValue><PeriodDisplayName /><PeriodType>duration</PeriodType><PeriodStartDate>2013-01-01T00:00:00</PeriodStartDate><PeriodEndDate>2013-06-29T00:00:00</PeriodEndDate><Segments /><Scenarios /></contextRef><UPS /><CurrencyCode /><OriginalCurrencyCode /></MCU><CurrencySymbol /><Labels><Label Key="CalendarSupplement" Id="0" Label="6 Months Ended" /><Label Key="Calendar" Id="1" Label="Jun. 29, 2013" /></Labels></Column></Columns><Rows><Row FlagID="0"><Id>1</Id><IsAbstractGroupTitle>true</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>1</Level><ElementName>us-gaap_DebtDisclosureAbstract</ElementName><ElementPrefix>us-gaap_</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText /><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>xbrli:stringItemType</ElementDataType><SimpleDataType>string</SimpleDataType><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Debt Disclosure [Abstract]</Label></Row><Row FlagID="0"><Id>2</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>2</Level><ElementName>us-gaap_DebtDisclosureTextBlock</ElementName><ElementPrefix>us-gaap_</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><PreferredLabelRole>terseLabel</PreferredLabelRole><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="D2013Q2YTD" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText>&lt;div style="font-family:Times New Roman;font-size:10pt;"&gt;&lt;table cellpadding="0" cellspacing="0" style="font-family:Times New Roman; font-size:10pt;"&gt;&lt;tr&gt;&lt;td style="width:36px;" rowspan="1" colspan="1"&gt;&lt;/td&gt;&lt;td rowspan="1" colspan="1"&gt;&lt;/td&gt;&lt;/tr&gt;&lt;tr&gt;&lt;td style="vertical-align:top" rowspan="1" colspan="1"&gt;&lt;div style="line-height:120%;font-size:10pt;padding-left:0px;"&gt;&lt;font style="font-family:inherit;font-size:10pt;font-weight:bold;text-align:justify;"&gt;&lt;/font&gt;&lt;/div&gt;&lt;/td&gt;&lt;td style="vertical-align:top;" rowspan="1" colspan="1"&gt;&lt;div style="line-height:120%;text-align:justify;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;font-weight:bold;text-align:justify;"&gt;Notes, Mortgage Notes and Obligations Payable&lt;/font&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;font-style:italic;text-decoration:underline;"&gt;Senior Secured Asset-Based Revolving Credit Facility (the "ABL Facility")&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;As of &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;June&amp;#160;29, 2013&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;, the Company had approximately &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$60.0 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; in outstanding borrowings, and approximately &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$13.1 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; in outstanding letters of credit, under the ABL Facility.  Based on the May 2013 borrowing base calculations, at &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;June&amp;#160;29, 2013&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;, the Company had excess availability of approximately &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$226.9 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; and approximately &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$189.4 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; of excess availability before triggering the cash deposit requirements under the ABL Facility.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;On July 31, 2013, the Company voluntarily repaid &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$10.0 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; of outstanding borrowings under its ABL Facility and, accordingly, has classified such amount as current maturities of long-term debt in the accompanying unaudited condensed consolidated balance sheet as of &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;June&amp;#160;29, 2013&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;font-style:italic;text-decoration:underline;"&gt;Debt Covenant Compliance&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;The indenture governing the &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;10%&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&amp;#160;Senior Notes due 2018 (the "&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;10%&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; Notes") contains certain restrictive financial and operating covenants including covenants that restrict, among other things, the payment of cash dividends, the incurrence of additional indebtedness, the making of certain investments, mergers, consolidations, and the sale of assets (all as defined in the indenture and other agreements).  As of &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;June&amp;#160;29, 2013&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;, the Company had the capacity to make certain payments, including dividends, under the &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;10%&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; Notes of approximately &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$53.1 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;.  &lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:36px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;As of &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;June&amp;#160;29, 2013&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;, the Company was in compliance with all covenants under the indentures that govern the &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;10%&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&amp;#160;Notes and the &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;8.5%&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; Senior Notes due 2021 (the "&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;8.5%&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; Notes") and the credit agreements that govern the ABL Facility and the &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#231f20;"&gt;senior secured term loan due 2017 ("&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;Term Loan Facility").&lt;/font&gt;&lt;/div&gt;&lt;/div&gt;</NonNumbericText><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>nonnum:textBlockItemType</ElementDataType><SimpleDataType>na</SimpleDataType><ElementDefenition>The entire disclosure for information about short-term and long-term debt arrangements, which includes amounts of borrowings under each line of credit, note payable, commercial paper issue, bonds indenture, debenture issue, own-share lending arrangements and any other contractual agreement to repay funds, and about the underlying arrangements, rationale for a classification as long-term, including repayment terms, interest rates, collateral provided, restrictions on use of assets and activities, whether or not in compliance with debt covenants, and other matters important to users of the financial statements, such as the effects of refinancing and noncompliance with debt covenants.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 505

 -SubTopic 10

 -Section 50

 -Paragraph 3

 -URI http://asc.fasb.org/extlink&amp;oid=6928386&amp;loc=d3e21475-112644



Reference 2: http://www.xbrl.org/2003/role/presentationRef

 -Publisher SEC

 -Name Regulation S-X (SX)

 -Number 210

 -Section 02

 -Paragraph 19, 20, 22

 -Article 5



Reference 3: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 210

 -SubTopic 10

 -Section S99

 -Paragraph 1

 -Subparagraph (SX 210.5-02.19,20,22)

 -URI http://asc.fasb.org/extlink&amp;oid=6877327&amp;loc=d3e13212-122682



</ElementReferences><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Notes, Mortgage Notes and Obligations Payable</Label></Row></Rows><Footnotes /><IsEquityReport>false</IsEquityReport><ReportName>Notes, Mortgage Notes and Obligations Payable</ReportName><MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel><SharesRoundingLevel>UnKnown</SharesRoundingLevel><PerShareRoundingLevel>UnKnown</PerShareRoundingLevel><ExchangeRateRoundingLevel>UnKnown</ExchangeRateRoundingLevel><HasCustomUnits>true</HasCustomUnits><IsEmbedReport>false</IsEmbedReport><IsMultiCurrency>false</IsMultiCurrency><ReportType>Notes</ReportType><RoleURI>http://www.nortek-inc.com/role/NotesMortgageNotesAndObligationsPayable</RoleURI><NumberOfCols>1</NumberOfCols><NumberOfRows>2</NumberOfRows></InstanceReport>
