My favorites so far have been:
1. World of Goo - Probably the most polished and interesting game available on WiiWare so far. Hard to go wrong here.
2. Mega Man 9 - Probably the best old-school Mega Man game I've played since... Mega Man 3? Yes, I think so. The achievements and bonus features are also a nice addition.
3. Swords & Soldiers - Gameplay is a bit simplistic, but still takes some skill to use your resources effectively. Who would've guessed that a 2D RTS could be so much fun?
4. Bit.Trip Beat/Core - Both awesome games, both at budget pricing. Beat is more interesting for me because of the control method, but Core has better graphics and is a better rhythm game.
5. Tetris Party - Do you like Tetris? This game has tons of features and a great price. The only downside is that the official tournaments are already done... but it's still worth buying for any Tetris fan.
6. Bonsai Barber - A game that encourages short, daily sessions to get the most out of it. Great character and production values, although the theme is completely wacky. Surprisingly good if you give it a chance.
Some games that are good, but not top notch:
1. Magnetica Twist - Controls were better than most reviews indicated, and this game ended up getting tremendous play time from my wife.
2. Art Style: Cubello - Oddly soothing. Not a lot of depth or complex strategy to this puzzle game, but still fun to play in short bursts.
3. Onslaught - FPS from WiiWare? Yes, and it's not a bad implementation. Complaints are that movement is slow and gameplay is quite straightforward... but a good choice as long as your expectations are reasonable going in. Online co-op and competitive multiplayer are a huge bonus, but no deathmatch mode. (For "deathmatch" FPS gameplay, maybe try Water Warfare instead.)
4. Final Fantasy: My Life as King - Personally, I prefer an actual RPG to the city management simulation this game provides... but this can be a pretty engrossing game if you get into it. The upcoming My Life as Darklord sequel looks more appealing for me. (For an actual RPG, check out FFIV: The After Years.)
5. LostWinds - Very very pretty game with interesting platforming mechanics. Slow pacing and lack of enemies make the game a bit easy, and it's also quite short. I'm happy to have it but don't think it would be everyone's cup of tea.
6. Toki Tori - Neat action/puzzler that can get fiendishly difficult in advanced levels. Production values are very nice, but I never quite enjoyed the game as much as some others.
Disappointments I had:
1. Bust-a-Move Plus - The local multiplayer is fun, but presentation is so-so and the single players "puzzles" are often impossible once you reach higher levels. Kind of makes the game feel a bit blargh if you ask me. Not worth buying.
2. Pool Revolution: Cue Sports - Not really bad, and at a great price point, but the motion controls just weren't as good as I wanted. Online play is a nice bonus though!
3. My Aquarium - Ok, I knew what I was buying and am really only disappointed that MP3 support wasn't included.
Regarding Star Soldier R, it's not bad at all but I think that getting the TG-16 game named Soldier Blade on the Virtual Console is a better deal. Very good game at a lower price, with both a score attack and campaign mode.
I'm itching to try Space Invaders Get Even, but the weird pricing model (with a need buy extra levels) has kept putting me off. One of these days, maybe.