X-Men: Mutant Academy (Crawfish Interactive/Activision, 2000)
1v1 fighter that has great menu music, but then terrible music in-game. Kind of like how it has bad character sprites mixed with great backgrounds, or how there's a surprising variety of moves, but crouching and punching is enough to crush the AI. A game of two halves.
X-Men: Mutant Wars (Avit Inc/Activision, 2000)
Despite the similar name, this has nothing to do with Mutant Academy. It's an incredibly basic brawler where the enemies mostly don't bother to attack and picking up health makes the game freeze for a whole second so it can adjust your XP. On top of all that, Wolverine here only seems to have one move.
X-Men: Wolverine's Rage (Digital Eclipse/Activision, 2001)
A mix of a brawler and platformer that doesn't do either genre well. It has a very basic set of attacking moves and imprecise jumps. Worst of all, the music might as well just be a sequence of random notes.
Xena: Warrior Princess (Titus Software, 2001)
A Zelda-like that might be okay. I'll never know, because it's another entry on today's list with terrible music. There's a backing instrument on every track that almost sounds like someone slowly sending a telegraph.
Xtreme Sports (WayForward/Infogrames, 2000)
A game about entering an extreme sports competition, which in practice means a bunch of different minigames. I played Skyboarding, which has you falling to the ground while collecting arrows to set up combo tricks. You can attempt to perform a combo at any time, but you'll lose all your arrows if your inputs are wrong or you hit an enemy, so there's some push-your-luck elements to it. Had a great time with it, so it's going on the list.
Xtreme Wheels (Spike/Bergsala, 2000)
Bergsala is Nintendo's distributor in Sweden, and Spike would later merge with Chunsoft and create some of my favorite games ever. You certainly wouldn't have been able to tell that from this game, though. It's Excitebike, but everyone is constantly falling off their bike, there are seemingly about 200 riders on the track, and you have a stamina bar that forces you to stop every now and then. Decent music, but not at all fun.
Yakochuu GB (Athena, 1999)
"Most unreadable Japanese font on GBC" is a competitive category, but this visual novel has a good claim to it. It has extremely obnoxious background noises as well, and it keeps those backgrounds around for way too long.
Yar's Revenge (Telegames, 1999)
Someone gave me this as a kid and I still have the original cart. You need to blast through the shield of the enemy base without getting hit by either the slow rectangular homing enemy or the fast dumbfired star enemy, or any number of other hazards on later levels. You can't shoot through the field in the middle of the map, and you need to physically touch the enemy base in order to unlock the missile that can kill it. Once you win, there are several hundred more levels.
Yogi Bear: Great Balloon Blast (ITL/Bam Entertainment, 2000)
The intro to this game makes it sound like it's going to be Balloon Fight, but then it's just this match 3 game that's shown up under a few different names on GBC. Unremarkable.
Yu-Gi-Oh! Dark Duel Stories (Konami, 2000)
It's Yu-Gi-Oh. This was the only one to release in the US, so anyone who cares about it is probably already familiar with the game. If not, it's basically a series of duels in which you have to beat each opponent five times. Sounds pretty tedious, and the interface and repetitive music probably wouldn't help.
Yu-Gi-Oh! Duel Monsters II: Dark Duel Stories (Konami, 1999)
This is actually the prequel to the game that released outside of Japan, confusingly. It's pretty much exactly the same game with different menus and fewer duelists to fight.
Yu-Gi-Oh! Duel Monsters 4: Battle of Great Duelists - Jounouchi Deck, Kaiba Deck, and Yuugi Deck (Konami, 2000)
The same game again, but now in three flavors that are each also the same game. As far as I can tell, the only differences are the color of the main menu and which cards you start with. It has six duelists to fight instead of the five or four in the last two games. Woohoo.
Golf Ou: The King of Golf
John Romero's Daikatana
Kakurenbou Battle Monster Tactics
Keitai Denju Telefang
The Legend of Zelda: Link's Awakening DX
The Legend of Zelda: Oracle of Ages
The Legend of Zelda: Oracle of Seasons
LEGO Island 2: The Brickster's Revenge
Metal Gear Solid
Millennium Winter Sports
Pokemon Crystal Version
Pokemon Card GB2 - GR Dan Sanjou!
Pokemon Puzzle Challenge
Pokemon Trading Card Game
Quest for Camelot
Return of the Ninja
Scooby Doo! Classic Creep Capers
SD Hiryuu no Ken EX
Shin Megami Tensei Devil Children: Aka no Shou
Space-Net: Cosmo Blue
Star Ocean: Blue Sphere
V-Rally: Edition '99
Wario Land II
Wario Land 3
Wendy: Every Witch Way