Which popular apps prevent sleep on Mac OS X?
Known to cause sleep issues:


Better Touch Tool: Even when it is disabled, as long as it's running, sleep mode won't work.
Stack Exchange Notifier: more info here.
Symantec Encryption Desktop: more info here, Symantec's Official Reason here.
NoSleep: App that does what it says.  Although this is the main purpose of the app, for troubleshooting purposes it's good to check whether it's installed and accidentally on ;-)


Could potentially cause issues:


Dropbox caused problems in Snow Leopard.
Spotlight can prevent sleep, especially if you just installed Mac OS X.


Apps that have never caused sleep issues: