Here's the list I submitted, in its entirety. I was out of the loop on the complete instructions, so if there was a limit of 3 per platform, I didn't know about it or perhaps brazenly ignored that rule.
Jonathan Metts – Best of 2009
Wii Games:
Silent Hill: Shattered Memories – This is a noble and arguably successful attempt to revive and reform the survival horror genre. While perhaps not actually scary, it is genuinely disturbing, shocking, and always interesting.
The Beatles: Rock Band – It was a very bad year for music games, but Harmonix still took their franchise to new heights with this partnership. There are no filler bands, and the visuals are actually worth paying attention to. Be sure to try some of Paul's bass lines.
Wii Sports Resort – This is a vastly improved sequel to Wii Sports. Yes, MotionPlus makes it feel different, but the games are also deeper and more diverse. Resort has a lot more single-player appeal, and it's still a great party game.
Excitebots: Trick Racing – You didn't play this game, but you should have. It is unfailingly wacky and consistently fun. There are tons of vehicles to unlock, and the online racing works great.
Little King's Story – The comparison to Pikmin is unavoidable, but this game secretly wants to be an RPG. The sense of progression and discovery is wonderful as you explore this cute, though dangerous, world.
[EDIT: So yeah, this means NSMBWii wasn't even in my Top 5 Wii games of 2009. But I still like it. Despite what some people say, it was a very strong year on both Nintendo systems.]
DS Games:
Retro Game Challenge – Here's a mini-game collection aimed squarely at older gamers, except that some of the segments are more like full games unto themselves. Gems like Guadia Quest and Haggleman 3 could almost stand alone as great purchases, but the collective package is even better.
Henry Hatsworth – This weird mash-up recalls ultra-hard, melee-based action games like the Mega Man Zero series… but with a puzzle game on the bottom. Push on through the nasty bosses to find upgrades that lead to brilliant secret levels.
Mario & Luigi: Bowser's Inside Story – Easily Nintendo's best RPG in years, this game cures its predecessor's pacing and balance problems. The sprite animation is some of the best ever seen. Plus, you get a huge dose of Bowser in his most hilarious role yet.
Grand Theft Auto: Chinatown Wars – Its special aura may be diluted with ports to other handhelds, but this surprisingly great GTA still works best on Nintendo DS. It's also way funnier than the latest console edition of the series.
Download (WiiWare):
NyxQuest – Can you play a challenging 2D platformer while also using the Wii Remote's pointer? Both the charming presentation and ingenious design are subtle, but you will eventually get on board.
Bit.Trip Void – Easily the best game yet in this rapid-fire series, Void adds a lot of complexity and strategy. It's also more forgiving than Beat or Core, without becoming too easy.
Swords & Soldiers – This funny little game proves that you can have interesting, challenging strategy gameplay on a 2D plane. By the time the screen fills with cartoonish characters, you'll be hooked.
LostWinds: Winter of the Melodias – Even if you never played the impressive (but extremely short) original LostWinds, this sequel is well worth trying. It's longer and denser, with good platforming and tons of tricky puzzles. The graphics and sound are also much better than you'd expect from a game that fits on WiiWare.