Income Taxes (Details 4) (USD $) In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2010
Income Taxes
NOL and capital loss carryforwards	$ 78,095	$ 69,252
Tax credit carryforwards	25,619	23,779
Debt repurchase premium	15,503	18,221
Estimated liabilities	14,165	15,819
Stock-based compensation	8,127	9,306
Reserves and allowances	5,805	2,409
Deferred revenue	6,792	584
Convertible note hedge	47	1,279
Other	2,137	1,950
Valuation allowances	(127,418)	(127,795)
Total deferred tax assets	28,872	14,804
Property, plant and equipment basis differences	(26,065)	(11,066)
Goodwill and intangible asset basis differences	(2,759)	(2,381)
Convertible debt discount	(48)	(1,357)
Indefinite lived intangible asset basis differences	(3,204)	(2,505)
Total deferred tax liabilities	(32,076)	(17,309)	0
Net deferred tax liability	$ (3,204)	$ (2,505)