Well I can tell you what I've done without any negative side affects.
Apps I install that require root:
Root explorer
ShootMe
AdFree
Apps I disabled via Root Explorer, by renaming the APK's from application.apk to application.apk.old:
amazonmp3
blockbuster
browser.apk (I use Dolphin)
DLNA
DLNASystemService
FMRadio
FMRadioService
HelpCenter
LiveWallpapers
LiveWallpapersPicker
MagicSmokeWallpapers
MediaGallery (I installed and use the Froyo gallery I posted in the apps section)
Mynet
Protips
QuickOffice (I use Docs to Go)
redding-7648-signed (Kindle)
Skype
StickNoteWidget
Above apps are in /system/app folder and require you to enable R/W for the folder in root explorer.
There's some other threads in this forum that warn you what not to remove, such as the Blur apps. Also, you'll notice that I rename files, I don't remove them. Much safer.