Here is my personal compatibility list for PJ64, based on games I have tested myself. I don't feel like downloading every game, so the list is not complete, but I do have most of the more popular games.
Playable--
Games that are totally playable with few or no issues. These games may or may not be playable to completion
1080 Snowboarding (JU) [!]
Banjo-Kazooie (U) [!]
BattleTanx (U) [!]
BattleTanx - Global Assault (U) [!]
BattleTanx - Global Assault (E) [!]
Beetle Adventure Racing! (U) [!]
Blast Corps (U) (1.0) [!]
Bomberman Hero (U) [!]
Buck Bumble (U) [!]
Castlevania (U) (V1.0) [!]
Castlevania - Legacy of Darkness (U) [!]
Conkers Bad Fur Day (U) [!]
Cruis'n World (U) [!]
Diddy Kong Racing (U) (V1.1) [!]
Donkey Kong 64 (U) [!]
Doom 64 (U) [!]
Duke Nukem - ZERO HOUR (E) [!]
Earthworm Jim 3D (U) [!]
Excitebike 64 (U) [!]
Extreme-G (U) [!]
Fighting Force 64 (U) [!]
Forsaken 64 (U) [!]
F-Zero X (U) [!]
Gex 3 - Deep Cover Gecko (U) [!]
Goemom's Great Adventure (U) [!]
GoldenEye 007 (u) [!]
Jet Force Gemini - Kiosk (U) [!]
Legend of Zelda, The - Ocarina of Time (U) (V1.0) [!]
Legend of Zelda 2, The - Majora's Mask (U) [!]
Mace - The Dark Age (U) [!]
Mario Golf (U) [!]
Mario Kart 64 (U) [!]
Mario Tennis (U) [!]
Mischief Makers (U) [!]
Mortal Kombat 4 (U) [!]
Mystical Ninja 2 - Starring Goemon (E) [!]
NFL Blitz 2000 (u) [!]
Nuclear Strike 64 (U) [!]
Paper Mario (U) [!]
Perfect Dark (V1.0) (U) [!]
Rayman 2 - The Great Escape (U) [!]
Road Rash 64 (U) [!]
Rocket - Robot on Wheels (U) [!]
RR64 - Ridge Racer 64 (U) [!]
Rush 2 - Extreme Racing USA (U) [!]
Shadow Man (U) [!]
Sin and Punishment - Tsumi To Batsu (J) [!]
Spacestation Silicon Valley (E) [!]
Spider-Man (U) [!]
Star Fox 64 (U) [!]
Star Wars - Shadows of the Empire (U) (V1.2) [!]
Super Mario 64 (U) [!]
Super Smash Bros. (U) [!] --
use 1.3 video
Tony Hawk's Pro Skater 2 (U) [!]
Top Gear Rally 2 (U) [!]
Turok - Dinosaur Hunter (U) (1.0) [!]
Turok 2 - Seeds of Evil (U) [!]
Turok 3 - Shadows of Oblivion (U) [!]
Turok 3 - Shadows of Oblivion (E) [!]
Wave Race 64 (U) (1.0) [!]
Playable, with errors--
Games that are playable with heavy or otherwise distracting errors
Killer Instinct Gold (U) (1.2) [!]--
graphics slow
Mystical Ninja - Starring Goemon (U) [!]--
graphics slow
Pilotwings 64 (U) [!]--
graphics slow, shadow
Quake 64 (U) [!]--
flicker
Quake II (U) [!]--
flicker, graphics slow
San Francisco Rush 2049 (U) [!]--
sound
Winback - Covert Operations (U) [!]--
Floating grey square? "force normal blending"
minimizes effect
World is Not Enough, The (U or E) [!]--
sound
Video Plugin Issues--
Games will run but with missing graphics in one or more areas
Extreme-G XG2 (U or E) [!]--
Menus ok, depth problem in-game
Glover (U or E) [!]--
access violation at end of 1st level
Hot Wheels Turbo Racing (U) [!]--
Menus missing, in-game ok
Kirby 64 - The Crystal Shards (U) [!]
Wipeout 64 (U) [!]--
Menus missing, in-game ok
Yoshi's Story (U) [!]
Not Supported--
Games that either will not run, or will run with severe problems
Banjo-Tooie (U) [!]
Body Harvest (U or E) [!]--
Use PJ64 v1.3
City Tour GP-All Japan Grand Touring Car Championship (J) [!]
Cruis'n USA (U) (V1.0) [!]--
Use PJ64 v1.3?
Cruis'n USA (E) [!]--
Use PJ64 v1.3?
Dark Rift (U or E) [!]
Disney's Tarzan (U) [!]
Duke Nukem - ZERO HOUR (U) [!]--
Use PAL
Gauntlet Legends (U) [!]
Indiana Jones and the Infernal Machine (U) [!]
Jet Force Gemini (U) [!]--
Control issues, use Kiosk
Kobe Bryant's NBA Courtside (U) [!]
Mia Hamm Soccer 64 (U) [!]
NightMare Creatures (U) [!]--
Use PJ64 v1.3?
Ogre Battle 64 - Person of Lordly Caliber (U) [!]
Resident Evil 2 (U) [!]
Spacestation Silicon Valley (U) [!]--
Use PAL
Star Wars - Rogue Squadron (U) [!]
Stunt Racer 64 (U) [!]
World Driver Championship (U) [!]