There are a lot of Game Boy and Game Boy Color games I'd love to play over again. However, I decided to go with "two" games that I know I'm somewhat in the minority about. I picked them not only because they're not as widely known, but because they have a reasonable shot of making it on the handheld rendition of Virtual Console. Both of those games wound up being pseudo-ports to the Game Boy Color: Crystalis and Mega Man Xtreme.
Yes, it's a bad port. Yes, it's got major flaws. However, Crystalis is just such a fantastic game that I don't care. Originally an SNK-published NES title from 1990, Crystalis on the Game Boy Color was developed by Nintendo Software Technology and released in 2000. The Game Boy Color version had to deal with reduced screen size that lead to enemies off screen hitting you, stupid "politically correct" plot changes, and an inferior soundtrack. However, the action-adventure/RPG hybrid gameplay is still fun. Bearing quite a bit in common with the gameplay of the 2D Zelda titles, Crystalis is a must own for fans of those games… even if the only way we get to play them is an emulated version of a bad port.

Those are tigermen. Kill them with extreme prejudice.
Would I rather get the NES version on Wii's Virtual Console? Sure. However, Nintendo bought the rights to Crystalis so they could have NST make the Game Boy version. If we're ever going to get Crystalis for download, it's going to be this version, and even with its flaws I'm okay with that.
Is it cheating to pick two games? Does it really matter when the games are Mega Man Xtreme and Xtreme 2? They're practically the same game. Sure the Mega Man games for the original Game Boy are the more respected handheld entries, but I never brought Mega Man 3 with me just for the music (very solid translations from the SNES source material). The first Xtreme title had some completely asinine plot where a rogue Reploid named Techno unleashed the defeated Mavericks from Mega Man X and X2 into the Mother Computer at Maverick Hunter Base. Both games feature levels lifted from the first few X titles, along with the bosses from those games. The Xtreme games also introduce (and see the end of) the Shadow Hunters, a group of ne'er-do-wells headed up by Zain and Geemel.
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I hate you both so much. At least neither of you are that jerk Gareth from Xtreme 2.
Xtreme 2 created the plot device of the "DNA Soul," which, when deprived of it, Reploids cease to function. The less spoken of that, the better. It also reintroduced us to playing as Zero (fitting since the game features X3 bosses, and that's the first time Zero could be used) and brings back Iris. I've never forgiven Xtreme 2 for bringing back Iris.
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For some reason Xtreme 2 reunites us with Zero's girlfriend. "WHAT ARE YOU HERE FOOOOOOOOOOOOARE?"
Even with the games being nothing more than reused, down-scaled SNES assets, they're fun games. I'd love to play them again, and given that Capcom loves to sell us Mega Man games as many times as they can, there's no reason to think they wouldn't be thrilled to sell us a game that was created as a way to sell us games we already bought on other hardware.

"...that jerk Gareth from Xtreme 2." You go to hell, Gareth!