I'd like my Option and Alt keys to switch places in certain applications. Is there any way to change the modifier keys according specific applications in Mac OS X?
Alternatively; is there "an application for that"?
It's difficult to tell what is being asked here. This question is ambiguous, vague, incomplete, overly broad, or rhetorical and cannot be reasonably answered in its current form. For help clarifying this question so that it can be reopened, see the FAQ.
I use Ukulele for a PC keymap (there are included Logitech keymaps for OSX86 users). DoubleCommand is a great app to swap Command, Option and Control, and it can correct the behavior of the Home/End keys on PC.
You may build a different keymap and switch keymap when you switch application. I don't know if Ukelele allows you to change the position of the modifiers key, but if it doesn't I guess you still can edit the XML by hand.
(still, I think you'd better accept the proper keys rather than doing this dirty workaround)