1) Replace the app's icon.png file. Name the icon you want icon.png and drop it inside of the app via SSH. You'll be asked to overwrite the original - do so.
2) If you don't want to totally loose the original icon, use WinterBoard. Create a theme ( a folder). Then, inside that folder, create another and call it "Icons". Inside that, place the icons you want to use, named appropriately. (An icon for the Phone app would be named Phone.png, and icon for Super Monkey Ball would be named Monkey Ball.png, etc. Whatever the app icon label is on the home screen, that's your name.) Themes can also include wallpapers, docks, and other images. WinterBoard themes go in this directory:
I can't figure this out for the life of me, but is there a website where you can download specific icons instead of making icons yourself? I find making icons very time consuming and while I'm not lazy, I just don't think I have the creativity like some people here do.