I actually like the stock messenger a lot, the ONLY feature I need from handcent is the pop up feature. I tried SMS pop up but it didn't clear my read message from the message icon on the home screen, and that annoyed me.
I also like how it shows a small version of the photo if you send one, instead of a little box that says 'slideshow'.
I am weird about using add ons when you have something there already, I hate having "un-needed stuff" on my phone (having the stupid footprints, twitter, nascar and football apps, make me mad too).
So sometimes I hate having to use handcent, I prefer to have ONE messenger program on there and use up less app space, but I need that pop up feature. Otherwise, I'd uninstall handcent and use a pop up app.