"Running smoothly" is relative. Exactly what issue(s) are you running into?
Avoid updating apps through iTunes on your iPhone. Try to update them on your pc/mac then this will update them through syncing. If you find backups take forever it is always because of a corrupt app on your iPhone.
Mine's been acting weird too, iTunes synch issues and what not.I've noticed my 3GS is getting very jerky. For example, when closing an app, the home screen doesn't fly in, it sort of jerks its way in.
It's definitely slowed down a lot (so much so I bought iStat to check it was using all the RAM).
Avoid updating apps through iTunes on your iPhone. Try to update them on your pc/mac then this will update them through syncing. If you find backups take forever it is always because of a corrupt app on your iPhone.