Well for graphics I recomend Glide 64 (don't let what it says it's called fool you). It has a load of options especially in texture filtering to make your games look better then ever. If you have a hard time with it you can try the officially compiled version here (it's just slightly older, only slightly).
If in the end you still can't get it running, try using these (second download link). They're semi-official bug fix release of the standard plugins, better then default. The graphics plugin for this might be better, because normally you can't force Anti-Aliasing or Vsync with Intel cards (from what I've seen) and sadly that's what you'd need to do for Glide 64, with the standard plugin AA and Vsync options are built in (with standard texture filtering which to some might look better anyways).
For audio, either the LLE built in plugin or the HLE (faster) plugin Azimer's HLE audio. In contrast to Glide 64 however, it only has 3 options to configure, and for the most part you shouldn't need to touch them.
For input there is nothing better then the N-Rage input plugin. It pretty much works with any controller, as well as supports controller extensions such as a Rumble Pak, a Mem Pak, or (sadly not and) a Transfer Pak (yes, it's pak, not pack). If you're using an Xbox controller, it even supports Xinput.
If you're willing to try out a (only slightly illegal) beta version try Project64 1.7.0 50b23 (hosted here on Emuparadise). It should have a bunch of prepackaged plugins, but Glide 64 and the N-Rage plugins are both outdated (the audio plugin is old as dirt and is the latest). It's the one I use, also if you do use it no need to download that semi-official bug fix release I was talking about, because this is better (or worse, it's a beta for results may vary depending on the game).
That's all I can think about adding on here, enjoy the wonderful world of N64 retro gaming (now in HD, maybe).