This is a fun platformer where you have to clone yourself to complete levels. It's pretty hard but there's a link to the walkthrough in the game.
http://www.kongregate.com/games/GregAnims/use-boxmen
A physics game where you have to arrange objects to guide the ball into a bucket. Sort of like The Incredible Machine.
http://dynamic.systems.fizzlebot.com/
There are a ton of multiplayer games on this site:
http://www.kongregate.com/multiplayer-games
You might be thinking of this one http://www.casualcollective.com/#games/Desktop_Armada
The new Gemcraft is out on armorgames. This one seems much harder than the first (which is a good thing IMO).
http://armorgames.com/play/3527/gemcraft-chapter-0
A fun little puzzle game on Kongregate. Use your sword to cut the chains and release the balls. Get the balls to the urn of the same color to complete the level.
Civiballs
Hex Empire
This is a great strategy game somewhat like Risk. You face three computer AI opponents, each with their own military and capitals. Your manpower grows as you capture towns. Ultimately, you have to capture all the enemy capitals.