you should be able to delete the entire emulators folder (or EMU) and not have it mess anything up....
I'd say don't dismiss and delete stuff unless you are really sure you aren't going to want to use it.
the apps don't take a lot of space to begin with and the Emus probably don't either unless you have PS1 and N64. I'd be willing to bet that they take at most a full DVD. I'd agree with FA that getting a newer/bigger/better hard drive is the way to go.
I agree even if he only has a retail HDD the amount of space likely taken up by Apps, even if that includes XBMC will probably be only a few hundred MB unless the latter came with a large set of skins, scripts etc.