It depends on what you consider a 'flaw'. In case you haven't suspected, there's a reason why plugin and emulator authors don't end up fixing emulation issues even though they are aware of them: It's hard. Sometimes, it's a matter of sacrificing speed for graphics or vice versa.
I haven't tested every dumped Nintendo 64 ROM out there, of course, but I can list a few games that I've noted to run flawlessly or with one or two very inconspicuous graphics glitches or small slowdowns:
- Banjo-Kazooie (Glide64 on Nemu64 emulator only or w/ No Sound by zilmar)
- Legend of Zelda, The: Ocarina of Time (Glide64)
- Legend of Zelda, The: Majora's Mask (Glide64 or maybe Direct64)
- Super Mario 64 (Glide64 or Direct64)
- Super Smash Bros. (glN64)
Yada, yada, yada, don't feel like listing them all. Too many that run flawlessly.

What would be the point? If you just want to run a certain Nintendo 64 ROM in particular, start a thread on it, and hopefully one of the experts will tell you how the game can be best (hint: not always perfectly) emulated.