Plugins are ROM sensitive normally, its all based on what plugin works best for what rom.
Example: South Park Rally shows up as UNSUPPORTED in the ROM list, however, this is only with Jabo's 3D6 1.5, using Glide64 + Evoodoo it works perfectly for me.
Or take Mario Tennis, without certain advanced settings applied, you get shoadows and a nasty replay effect, So it all depends on the games you want to play.
As a good start point, Glide 64 + Evoodoo and Jabo's 3D6 1.5 are your 2 best video plugins, IMHO. Rice's Dedalus also arent bad.
Sound typiclaly doesnt matter, except for hydrothunder, where you need to use No Audio Plugin 2.0 for 1964 to get it to work, and you also need to use Evoodoo + Glide, at least I do anyways.
Controller Plugins are a matter of opinion or use, use N-Rage's plugin to emulate Transfer packs (for pokemon stadium 1 and 2) it will also fake the console into thinking youre using a rumble pack should you not have one or the means to use one (for chameleon twist) and It supports mem pack emulation, (saves to hard disk) I like NRage's plugin best for my controller.
Hope this helps.