Uninstalled Java, but my apps still work??

I'm wondering if there's something I'm not looking for -- some way Java can start up.
I uninstalled it and I don't understand why some Java-based apps still work.
How is that possible?
The reason I care about this is because I removed Java in response to a virus.
I haven't found traces of the virus (possibly "Win32/TrojanDownloader.Agent.PDF trojan") anymore.
I've used all kinds of utils to get rid of it:
Manually: ProcessExplorer, HiJackThis, Process Scanner
Automated: NOD32, Malwarebytes, Ad-Aware, Spybot, TrojanHunter, Trojan Remover
I uninstalled Java with Windows Add/Remove.
And I don't have any "Java"-titled processes listed as currently running in my Windows Task Manager.
But now some Java programs work and some say they can't find Java.
Working: OpenOffice, FileZilla
Not Working: jEdit, Spark, DirSyncPro
I just noticed and deleted some "java" titled items in my Prefetch directory.
I'll restart now.

Ok, nothing reappeared in the "Prefetch" directory, but OpenOffice and FileZilla both work fine.

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Uninstalled Java, but my apps still work??

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