warioland II is a must over 50 levels of wario goodnesss!
For that matter: Warioland 3 (not Super Mario Land 3: Warioland, although, that's a pretty good game too).
Metal Gear Solid (Metal Gear: Ghost Babel, actually) if you can get hold of it
When the GBA was first released a local
Zellers was trying to liquidate it's GBC game stock and my dad saw some of the games and bought them for me. One of the games was Metal Gear Solid. For $5.
Love that game. Was released too late in the GBC cycle though. Sadly, that happens all the time to good games; just when they're getting it right on that system, the next iteration is released/announced and everyone ignores any new games for the old one.
EDIT: Also I guess people were sceptical of a portable MGS...