I installed this last night (version 3.0) and ended up screwing up my 3GS to the point where I had to restore. Everything seemed to be working fine until I realized that simply installing it changed some of my settings. One in particular was double-tapping the home button. Rather than double-tapping for phone favorites or bringing up iPod controls if music is running, it would only do one or the other. Not both. It also screwed up respringing Springboard. Springboard would respring, but would never take me to the lock screen. So after "respringing", I'd be at my home screen but couldn't tap on any icons until I put it to sleep and unlocked it.
To try and fix these issues (along with others...) I read on a forum that I should try resetting my settings. So, I did that.... and my iPhone never came back on. It just kept flipping between the Apple logo and a black screen. I had to put it in restore mode twice to force it to restore but finally got it going.
Moral of the story: don't install Supreme Preferences. You won't use most of them anyway.