Game Boy Color
Nintendo took a slow approach to publishing Game Boy Color titles on 3DS — there were only six available by 3DS VC's first anniversary, versus several dozen original Game Boy titles — and by the time GBC releases took off in earnest, Virtual Console had already loaded up on NES. For the most part, that made GBC a bit of a hard sell... though there certainly were exceptions, and a fair few essentials as well.
Harvest Moon 3
Harvest Moon and portable systems have always been one of those peanut-butter-and-chocolate gaming combos, and any Game Boy HM will do you right. But why not just go directly for the best and most refined one?
Nintendo's golf game has been strong from the very beginning, but it's hard to beat Mario Golf, which excellent combines Nintendo's great golf mechanics with Camelot's rich RPG experience.
Likewise Mario Tennis, which goes light on the RPG elements in favor of excellent gameply embellished with outlandish Mario power-ups. Not a traditional take on tennis, but a great one nevertheless.
Pokémon Trading Card Game
Who needs to drop big bucks on Hearthstone or even a real-life holofoil Charizard card when you can get a full video CCG fix for a single, reasonably priced transaction?
Pokémon Yellow Version
Game Freak/Nintendo, 1999
Some people Red and Blue, while other swear by Yellow. Either way, it's the same general first-gen content... the different being that this one takes influence from the anime, with a heavy emphasis on your mandatory pikachu starter.
The last great 8-bit game, Shantae flew beneath the radar for years only to become a hot-ticket item on the aftermarket. It's not as polished as its sequels, but WayForward's breakout creation remains a wonderful tribute to ’80s metroidvania classics like Wonder Boy III and The Battle of Olympus.
Super Mario Bros. Deluxe
This would be the definitive version of Super Mario Bros. if not for the reduced pixel resolution. But it includes so many goodies that you still need to own it: Save slots! Bonus collectibles! Oh, and the entirety of Super Mario Bros.: The Lost Levels as an unlockable.
The Legend of Zelda: Link's Awakening DX
While the color reissue of The Legend of Zelda: Link's Awakening didn't radically shake up the original game, one could make a strong argument that the original didn't need shaking up. An absolute masterpiece that was for portable games what A Link to the Past was for the Super NES.
The Legend of Zelda: Oracle of Ages/Oracle of Seasons
While not really on par with Link's Awakening (few games are), this color duology demands attention anyway. Together, they paint a perfect picture of Zelda as it was (Oracle of Seasons, based on 8-bit Zelda) and as it is (Oracle of Ages, based on the 64-bit era). Plus, beat one game and you can unlock the true ending in the other.
Two Tribes/Capcom, 2002
A clever little puzzle platformer, this late-bloomer was the debut title of soon-to-retire studio Two Tribes. Before you tuck into their swan song Rive, why not go back to where it all began?
Wario Land II
Finally, the Mario Land series comes into its own... by completely dropping Mario and focusing on the villain. Wario Land II radically changes the rules of the game, giving players an invincible hero whose comical reactions to abuse become platforming puzzles. A truly unique, and essential, work.
Wario Land 3
Bionic Commando: Elite Forces
The first proper attempt at creating a Bionic Commando sequel, this adventure lacks the near-perfection of its monochrome predecessor, despite featuring some clever ideas. A fun game, but if you have to go with just one, go with the original.
Game & Watch Gallery 2
Another collection based on Nintendo's old-school LCD games, offering both "original" and "arranged" versions. This time, the arranged versions feature color. The downside: It attempts to capture the dual-screen Donkey Kong handheld on a single-screen system.
Game & Watch Gallery 3
Third verse, same as the first (and second): Lots of classic G&W remakes here, in two different renditions, with dual-screen games being somewhat imperfectly served here.
The farming/life/marriage sim's first portable outing, it's both addictive and entertaining... just not quite as good as the third entry. You can't go wrong by owning any of them, really.
Harvest Moon 2
Hmm, is there an echo in here?
Legend of the River King
A sort of counterpart to Harvest Moon, Legend of the River King takes a similar low-key RPG/simulation approach to the sport of fishing. Japanese game developers love fishing, and that affection shows through here.
Legend of the River King 2
Also like Harvest Moon, the two River King games are ultimately very similar to one another. Get one or both and either way you'll feel good about life.
Lufia: The Legend Returns
A portable sequel of sorts to the cult favorite Super NES RPGs, this Lufia manages to cram a lot into a Game Boy Color cartridge... though it pads things out somewhat with boring procedurally generated dungeons, which drags the whole thing down a notch.
Mega Man Xtreme 2
The Xtreme games attempted to do for Mega Man X what the monochrome Mega Mans did for the NES games. Unfortunately, MMX was maybe just a bit too complex for Game Boy Color to handle... but despite that, Xtreme 2 makes a brave attempt and isn't too shabby, all in all.
Pokémon Puzzle Challenge
Intelligent Systems/Nintendo, 2000
Well, it's Tetris Attack, with Pokémon. Not the greatest puzzle series ever, but plenty of fun. Especially if you are obsessed with anything Pokémon.
Save Your Cash
Blaster Master: Enemy Below
A portable rendition of the NES classic. Great! But it brings nothing new to the table, so just get the original NES game instead.
Mega Man Xtreme
Where the second Xtreme turned out to be surprisingly fun, this first attempt fell flat. You could argue that bad Mega Man is better than no Mega Man, but it's not kind to deceive yourself in this way.
Prince of Persia
Ed Magnin/Red Orb, 1999
The classic PC platform adventure got a decent port to Game Boy Color... but there are so many better versions of this game out there, why subject yourself to this dud?