I'll second these games:
Mario 64
Ocarina of Time
Majora's Mask. Only a few dungeons, but they're EXCELLENT dungeons.
Star Fox 64 (Or is that the same as Lylat Wars in another country?)
Goldeneye
Perfect Dark
Smash Brothers
I'll second Mario Kart as well, especially since you haven't played Double Dash on the GC yet. It's a hard step back once you have. It does have much better multiplayer arenas on the 64, though.
Other suggestions:
Killer Instinct Gold
Mortal Kombat Trilogy
Those seem to be the last of the decent 2D fighters, IMO.
F-Zero X
Of course....you could just bypass all this trouble, find an adaptoid (a GENUINE adaptoid) and N64 controller on ebay, and load up project64 on your PC. It looks like that'll run you anywhere between $70-$100, depending on shipping charges. Most adaptoids are running around $50, and controllers are what, $5-10? Maybe $15.
I have Perfect Dark (American version). You want it? It looks like you need the PAL stuff, though. Anyway, pay shipping, and it's yours. I think it's complete too. (I had it boxed up, hoping its value went up. It never did.)
Hit up gamefaqs.com for instructions. Most games have at least a few FAQs that tediously list even the simple instructions found in the manuals, many times with more information about them.