Hmmmmm. . .it depends on what you're looking for. Gemcraft is a good general go-to, desktop tower defense is good too, and crop circles is perfect if you want an easy, yet fun and innovative way to play a TD.
well the original tower defence was elemental flash TD which i thougt was IMMENSE! i think it was inspired by the similar 'minigame' on warcraft.... anyway, since then many others have been developed with other features. gemcraft is great in some aspects, especially the upgrades deature, i like that but i think desktop TD, where you have to make a maze with the towers, and onslaught (and onslaught2), which just gets CRAZY!! have more engaging gameplay
Flash: desktop tower defensehas by a wide margin the best gameplay for a simple flash game.
3D: Downtown Defender, this is an almost console level of play, but its still in-browser (albeit with a plugin download) really immersive 3d experience.
Well I'd have to agree with thisisnotalt. Gemcraft is a good TD game. Seems to be the most popular, or at least has the highest play count of any AG TD game, probably also because of having to keep going back to it to get further in the game.
I also like the TD's like desktop TD where you make a maze with the towers. And Crop Circles wasn't bad, and it was nice and easy, so you didn't have to work as hard.
There's quite a few good ones, so you can't really choose one, but if I had to choose one, it'd be Gemcraft because of how you can combine different gems to make gems with multiple effects.