Yeah, everything installed except for what comes on it originally will be wiped.
And it depends. If whatever you have has infected all the programs, then yes. Though, I've not had a virus do that to me, so I don't know what to tell you in that case..
If I wipe, I have a disc with all the stuff I install (except for my Photoshop, I need make a disc for that) and reinstall it all, and it's fine.