Here are a few:
They are always on my EDGE Flash card:
GBC Games (with LameBoy):
Dragon Warrior 1 & 2
Dragon Warrior 3
Dragon Warrior Monsters
Dragon Warrior Monsters 2 - Cobi's Journey
Dragon Warrior Monsters 2 - Tara's Adventure
Legend of Zelda - Oracle of Ages
Legend of Zelda - Oracle of Seasons
Lufia - the Legend Returns
Magi-Nation
Pokemon Crystal
Pokemon Gold
PokeMon Silver
Pokemon Yellow
GBA Games (for 3in1):
Breath of Fire II
Breath of Fire
Dragon Quest Monsters - Caravan Heart (J2E)
Final Fantasy 1 And 2
Final Fantasy V
Final Fantasy VI
Golden Sun - The Lost Age
Golden Sun
Kingdom Hearts - Chain of Memories
Legend of Zelda - A Link to the Past & Four Swords
Legend of Zelda - The Minish Cap
Lufia - The Ruins of Lore
Pokemon Emerald
Pokemon Fire Red
Pokemon Leaf Green
Pokemon Ruby
Pokemon Sapphire
Sword of Mana
Tales of Phantasia
Also Chrono Cross, BOF3, BOF4, DW7 & DW8 (Some of these, like DW8, may be asking for too much).