Took me a bit to figure this out, but it's possible.
1) open Applications (your app drawer).
2) press Menu key.
3) press edit** - by default this will pop up with a box that says You need to switch the view type to customizable grid... click Switch.
**if you do not see the edit option, you are probably in the Alphabetical List View Type - change it to Customizable Grid, now press Menu, then Edit.
4) now, navigate to app you want on your main home row and drag it on top of app you want to replace, ie: Handcent SMS on top of the stock Messaging app.
5) click Menu, then Save, or just press your Home key and it should apply.