One of my favorite online games was Sacred Seasons, which was relatively fun to play but then before the first game was fully developed, they created the second one, which wasn't appealing to me and about 70 of the other 5 000 who played the game, so it just want dead, now I don't play it since there's only around twenty people on at a time.
Epic War series - Epic War 2 was my favourite, however if you haven't played any of them Epic War 4 and 3 would be great, personally they were a step down from Epic War 2 but it's nice to see indocg experiment. Sonny series - I'm not a fan for turn-based games but hell... I remember the Sonny section before where it would only be about Sonny, I remember making connections between the aspects of the game and hell it was great. I made multiple different ones and the mystery is great.
Battle Dawn - This is like a Turn-based MMORTS, it's free, it's on Kongregate (you need an account) and it can be found here.
Personally some of the music pieces are AMAZING and I love the aspect of it all where as a single player you cannot win. Plus if you don't have a lot of time on your hands you can pick servers which go slower than others.
Bubble Tanks series - You can see the games getting better as you go along, Bubble Tanks 3 has introduced all new weapons which is incredibly good to see. I hope to see a Bubble Tanks 4 with all the buyable weapons from Bubble Tanks 3 in it.
Colony - It has multiplayer, what else can I say?
Oh, and the fact that you must use cooperation for maximized awesomesauce is incredibly cool to see on a Flash game.
They are all exceptional games in their own right.