Stuff I like:
Pinball Pulse is probably the single greatest game of the service for reasons explained well above. One of my favorite video tables ever.
From Q Games: X-Scape and Trajectile are two of my very favorite games on the service. They're extremely well-made games; the only way you could not like them is that you just don't care for the gameplay (or, with X-Scape, the really odd graphic style).
From Wayforward: Mighty Flip Champs and Shantae are excellent as well, and I think each has an official thread.
Dark Void Zero is a must-play if you like fake NES games and quality shooting Metroidesque platformers.
Number Battle is exactly what the title implies: a really ingenious implementation of offensive number chaining. Some really crazy stuff is possible in this game. It made me sorry the original game that this is a stripped-down version of never came out in the US.
Mario vs DK is an excellent iteration. Totally on the Lemmings side - there is no Mario. But definitely worth checking out if you liked the GBA one or the Lemmings games.
Robot Rescue is a really awful looking and sounding game that has wonderful gameplay if you like the classic 90s style of single-screen careful-movement puzzlers. Also $2.
Spotto is good fun for $2, but Trajectile is the better blowing-stuff-up choice. Paper Plane and Pyoro 1/2 (aka Bird and Beans) are great too.
The Nintendo solitaire, for $2, is really lacking options, but it's pretty polished. I don't know if there are better options.
Stuff I don't:
Avoid ALL camera games. WarioWare Snapped and... the storybook one, whatever it was called, just do not work in any lighting environment I could give them. Maybe they would work outside, or on a fully-lit stage. I dunno. Just avoid, probably.
Link & Launch I could not get into at all. Just felt a little too hard and a little too random to me. You can learn the levels and do better, but it wasn't worth the work.
AIRace Tunnel is a really fun, braindead tunnel-flight game. It was a $2 teaser for a full racing game that didn't seem as fun.
Chronos Twin is a pretty cool idea that just didn't work for me in reality. I hear the Wii version is much easier to wrap your head around.
I wanted to love A Kappa's Trail, but it was probably my biggest disappointment (since my expectations were high). Beautiful art and an interesting concept. But towards the end, it just got too frustrating. The indirect controls make this a really fiddly experience, it's often hard to determine exactly where you went wrong, and the penalty for losing a level is starting it over again. You'll see how irritating it can be if you try it. But the title screen is great fun!
In between:
ArtStyle is a mixed bag. I loved the initial GBA crop, but the WiiWare and DSiWare ones have been more uneven. BoxLife and Pictobits are solid gold. Zengage is really good, if you like the style of puzzler. Base 10 was really likeable sometimes, but really frustrating, and despite a lot of effort I never got the hang of it - maybe I'm not smart enough. Digidrive I played too much of on the GBA, but it's great. Once you get the hang of it, though, there's little incentive to keep playing. Aquia was pretty, but the gameplay was way too random for me, but again maybe I just suck at it. And if you've ever played Intelligent Qube, Precipice may strike you as it struck me: as a really frustrating and sub-par imitator.
Aura Aura Climber was definitely worthwhile for $2, but, though I liked it, it never really gelled. The overall vibe isn't far from Flingsmash, though it's a better game than that.
Nongames
Art Academy is pretty awesome. There's no reason to buy both unless you really want the extra lessons, though.
The Mario alarm clock is a lot better than the built-in one, if you ever need an extra alarm clock around.
The Nintendo instrument tuner and metronome aren't half bad for the money.
I've heard good things about the dominant series of music programs, but I haven't plucked up the courage and points to download them yet. I'm really looking forward to trial versions on the 3DS eShop.