I'm not saying don't use them, but realize there is a performance loss for running apps continuously, obvious right? I use a few, gtalk, and gmail but I can live with the slight performance loss I've had so far, I don't notice it but I know it is there.I do not use any "so and so replacement", homescreen, texting, etc and I have not had any problems with speed or choppiness on my phone.
These apps that run as replacements, you are putting a lot of trust into the programmer to make it good code that will not lag your phone.
This also goes for other apps that run ALL the time, weather app, TASK KILLERS. By installing them you are putting the performance of your phone in their hands.
Next time you feel your phone getting laggy see if you have an app like this installed, it is the problem.
IMO the best custom launcher is Koush's, Task Killers will mess your day up, and it is good to have spare parts installed so you can keep launcher in memory.
A few other apps I can think of would be Facebook with notifications on, Twitter apps that notify you of updates.