I usually didn't give lesser known GB games a second glance. There were a few movie tie in games I enjoyed.
The Jurassic Park game comes to mind. I hear Gargoyles quest might be on the way for 3ds VC. That's one I totally missed.
Looking forward to it.
Can you think of any other GB games that didn't get the attention they deserved?

I remember Nintendo Power talking about Mole Mania which was a game that came out for the Game Boy in 1997 and was overlooked, and it was supposed to be a new Nintendo IP! That would be cool if that would be available on the eShop someday.

Metal walker

Battle Bull was a lot of fun.

Kirby's Pinball Land comes to mind.
I don't know exactly if i ever played any Pinball game or table before it. But at least it was the first level based Pinball experience i had.
If you don't absolutely hate the idea of Pinball-mechanics i recommend trying it. It's a very unique experience that tops Metroid Prime Pinball & Mario Pinball Land / Super Mario Ball _{(that one easily)} and is up there with the best Game Boy games in my opinion. _{Can't compare it to the Pokémon Pinball games though since i haven't played them yet.}

PS: How often can one write the word Pinball without being mistaken for Pete Townshend ?

I loved Skate or Die: Bad N Rad. It was a really challenging game, and it took me years to eventually complete it.

Not sure it's stood the test of time, but I remember enjoying Cosmo Tank as a kid.

Why does Metal Walker look like Metaknight!

Conker's Pocket Tales

Before he became the nasty little thing he is today.

I HAVE THIS GAME. ._.

It won't come to Virtual Console, but I think Darkwing Duck is a good Game Boy port of a good NES game.

I was really disappointed with Cosmo Tank. I remember I traded it for Dr. Mario, and I felt guilty for sticking the other kid with that game.

Agreed the Ducktales game wasnt bad either.

I liked the Space Invaders Game boy color Remake:
http://pocketmedia.ign.com/pocket/image/object/012/012328/603...

Heh, I was going to suggest Mole Mania, but it looks like they've beaten me to it. Mole Mania was a great puzzle game in the vein of Lolo, and it was helmed by Miyamoto himself. I don't know why they didn't advertise it more. It was brimming with charm and quality from beginning to end. I would definitely get it for the 3DS virtual console should it ever appear there.
Also:

• Kirby's Block Ball.
• Kirby's Tilt & Tumble (I'm assuming it could be done using 3DS's gyroscopic stuff).
• Shantae.
• Wendy: Every Witch Way (a neat platformer by the makers of Shantae).

I had this game.

I did not like this game. At all.

Rembered one more.
I don't know how well it fares to other versions of the game and i think i've never made through the whole game. But Cannon Fodder was a very fun game on the GBC.

Yes, I agree about these movie tie in games.

1) Darkman - an awesome platformer / brawler. by Ocean. Loved it to death. Still play it sometimes.
http://www.youtube.com/watch?v=S3c1pZPzNTQ

2) This I really like:
http://en.wikipedia.org/wiki/Tiny_Toon_Adventures:_Babs%27_Bi...

3) And I generally like platformers/beat em ups on the gameboy. Which is why I enjoyed The Simpons' Escape from Camp Deadly too and other platformers.

There are many other games but if I had to choose one overlooked game by Nintendo, it's Solar Striker. Have it in my multi-cartidge. Awesome music and addicting vertical shooter...
http://en.wikipedia.org/wiki/Solar_Striker

What good beat-'em-ups are there for GB/GBC that don't have superior console versions?

if you want to play on the go and like playing on the gameboy, with all its associated fun, then these beat em ups are a lot of fun.