It's got to be NA for me in the end, though there's quite a few JP games that I haven't played yet. Rough ranking of my faves from this year:
Ape Escape - PS1 (Japan Studio (Sony))
Gran Turismo 2 - PS1 (Polyphony Digital (Sony))
Bangai-O/Bakuretsu Muteki Bangai-O - DC/N64 (Treasure)
Ace Combat 3: Electrosphere - PS1 (Namco)
Bomberman 64: The Second Attack! - N64 (Hudson Soft/Hudson)
SoulCalibur - DC (1998 ARC port w/ some differences, Namco)
ChuChu Rocket! - DC (Sonic Team)
Dungeons & Dragons Collection - SAT (1994/1996 ARC ports, Capcom) - 3.85
Metal Slug X - ARC/NG (PS1 2000, SNK)
Crazy Taxi - ARC (Sega AM3)
Lunar 2: Eternal Blue/Lunar 2: Eternal Blue Complete - PS1 (1998 SAT port, Game Arts, MCD original by Studio Alex)
Ferrari F355 Challenge - ARC (Sega AM2)
Grandia - PS1 (1997 SAT port, Game Arts)
Strider 2 - ARC (PS1 2000, Capcom)
Final Fantasy VIII - PS1 (Square)
Front Mission 3 - PS1 (Square)
Game & Watch Gallery 3 - GBC (TOSE)
Mario Golf - GBC (different, Camelot Software Planning)
Mario Golf - N64 (Camelot Software Planning)
Omega Boost - PS1 (Polyphony Digital (Sony))
The House of the Dead 2 - DC (1998 ARC port, CRI, originally by Sega AM1 & Sega AM4)
Metal Gear Solid Integral - PS1 (PC 2000, Konami Computer Entertainment Japan)
Monster Rancher 2 - PS1 (Tecmo)
Pokemon Snap - N64 (HAL Labs)
Resident Evil 2 - DC/N64/WIN (1998 PS1 port, Capcom)
Shock Troopers: 2nd Squad (Shock Troopers 2) - NG (1998 ARC port, Saurus)
Tekken Tag Tournament - ARC (PS2 2000, Namco)
Space Channel 5 - DC (Sega Software R&D Dept. 9)
Street Fighter Alpha 3/Street Fighter Zero 3 - DC/SAT (1998 ARC port, Capcom)
Super Smash Bros. - N64 (HAL Laboratory, Creatures Inc. & Game Freak)
The Misadventures of Tron Bonne - PS1 (Capcom Production Studio 2)
Threads of Fate - PS1 (Square Product Development Division 3)
Um Jammer Lammy - PS1 (NanaOn-Sha)
Valkyrie Profile - PS1 (Tri-Ace)
Virtua Tennis/Power Smash - ARC (DC 2000, Sega Software R&D Dept. 3)
Baldur's Gate: Tales of the Sword Coast Expansion - WIN (BioWare - Canada)
Heroes of Might and Magic III: The Restoration of Erathia - WIN (New World Computing)
Unreal Tournament - WIN (Epic Games & Digital Extremes)
Age of Empires II: The Age of Kings - WIN (Ensemble Studios)
System Shock 2 - WIN (Irrational Games & Looking Glass Studios)
Command & Conquer: Tiberian Sun - WIN (Westwood Studios)
Heroes of Might and Magic III: Armageddon's Blade Expansion - WIN (New World Computing)
Homeworld - WIN (Relic Entertainment - Canada)
SimCity 3000 - WIN (Maxis)
Tom Clancy's Rainbow Six: Rogue Spear - WIN (Red Storm Entertainment)
Tony Hawk's Pro Skater - PS1 (Neversoft)
Spyro 2: Ripto's Rage! - PS1 (Insomniac Games)
Half-Life: Counter Strike - WIN (Mod, Minh "Gooseman" Le and Jess Cliffe, original game by Valve)
Hydro Thunder - ARC (Midway Games)
Jazz Jackrabbit 2: The Secret Files - WIN (JJ2+one new episode, Epic MegaGames)
Unreal Gold - WIN (incl Unreal Mission Pack: Return to Na Pali, Legend Entertainment (Expansion), original by Epic Games & Digital Extremes)
Tyrian 2000 - WIN (adds a 5th episode+new modes and ships, Eclipse Software)
Quake III: Arena - WIN (DC 2000, id Software)
Crash Team Racing/CTR: Crash Team Racing - PS1 (Naughty Dog)
Legacy of Kain: Soul Reaver - PS1/WIN (DC 2000, Crystal Dynamics)
Gauntlet Legends - N64 (1998 ARC port, Atari Games)
Planescape: Torment - WIN (Black Isle Studios)
Nuclear Strike 64 - N64 (Pacific Coast Power & Light (?), originally by Electronic Arts)
Star Trek: The Next Generation: Birth of the Federation - WIN (MicroProse)
Syphon Filter - PS1 (Eidetic)
Hydro Thunder - DC (ARC port, Eurocom Entertainment Software, originally by Midway Games)
Pharaoh - WIN (Impressions Games (Sierra))
Shadow Man - N64/WIN (Acclaim Studios Teesside - UK-based)
Aliens Versus Predator - WIN (Rebellion Developments)
Dungeon Keeper 2 - WIN (Bullfrog Productions)
Rayman 2: The Great Escape - WIN/N64 (Ubi Pictures/Ubisoft Montpellier)
Driver - PS1 (Reflections Interactive/Ubisoft Reflections)
Outcast - WIN (Appeal - Belgium)
Tomb Raider II Gold/Tomb Raider II: Golden Mask - WIN (5 new levels, Core Design) - 3.89
Wipeout 3 - PS1 (Psygnosis)
Worms: Armageddon - DC/N64/WIN (originally on PC, Team17 WIN etc./Infogrames N64)