If you're not quite sure what to drop or not, I would stay out of the registry. The "startup" tab of MSConfig should address any and all programs that are being started by the registry, as well as any Windows 3.x legacy programs that start from Win.ini., but when you uncheck them, it makes it quite easy to put them back if you make a mistake. If you scrub them from the registry and then find you need them, you might end up having to reinstall something.
If you have unchecked items that run from the startup folder, make sure you go to the start menu and delete them from the new folder "disabled startup items" that MSConfig creates. If you have to disable a start-menu program a second time, MSconfig will refuse to do it if it finds a copy already in the disabled folder.
Usually the only things that absolutely must run to make Windows go are Explorer and System tray. Usually you can figure out what other items belong to the antivirus program by looking at the folders they live in. If you're connecting to a broadband connection on Win 98 or 95, there may also be components of that that you must leave in.
If you stick to MSConfig, at least for starters, you can experiment. Uncheck a slew of things, boot up, and see if everything works properly. If it doesn't, you can usually get a clue from the error messages what needs to be rechecked. Keep that up until you're leaned out. Once you're sure, you can then attack the registry if you feel like it, or just leave it as is.
As Tucker notes, some programs you uncheck might be rechecked by parent programs that run either at startup or another time. If programs seem to be rechecking themselves, you'll have to find the program that is doing it, and either delete it or not run it, or get used to it. Quicktime is one of those - when run it will often recheck itself.