Have you ever tired Shadow Watch? Personal favorite of mine, and designed by a forum regular.
As mentioned above, Land of Legends is a commercially available indie in the vein of Advance Wars.
Tactics 100 Live is a Flash game that’s decent but a little lean.
PoxNora is an incredibly varied CCG/tactics game that allows you to play free with a starter deck. Fun and deep, but matches can sometimes take a while.
Modern Tactics 2 is a relatively deep Flash tactics game. Its cousin, Knight Tactics, tries to rip off a great game (FFT), but is missing a lot of key elements.
Over the years I’ve logged hundreds and hundreds of matches of Laser Squad Nemesis, which is PBEM but still awesome and innovative.
And I haven’t played Tactics Arena Online, but I’m thinking about giving it a try.
Freedom Force and Freedom Force vs. the Third Reich are terrific tactical games, and while not turn-based they can be slowed down and paused with ease.
I assume you’re aware of X-Com, Jagged Alliance, and Silent Storm…