Okay, some extra shit:
Continuity:
http://www.kongregate.com/games/glimajr/continuity - puzzle platformer. It has intereting idea of sliding screens to make paths for you to go and nice sounds. But I found controls rather lacking and level design shit. Its also tedious when you need to rotate screens multiple times. There is also a sequel on shitphones
https://itunes.apple.com/us/app/continuity-2-continuation/id432555999?mt=8 maybe it plays better on it.
Shift series:
http://www.kongregate.com/games/ArmorGames/shift - there are 4 parts in total. Another puzzle platformer where you basically shift your position and try to get out. With each new part (or sequel if you want) more complexities are added which naturally increases difficulty. Personally I think Shift 3 is the best one, additionally it has some preselected user made levels and some of them are very cool. For my taste fourth part adds too much shit with multiple controllable characters and preselected user levels aren't as cool.
Kingdoms Rush:
Yes, probably everyone played it already who gives 2 shits about Flash games, anyway I'm not sure if sequel's and clones were mentioned.
http://www.kongregate.com/games/Ironhidegames/kingdom-rush-frontiers - sequel by same guys, basically more of the same but I found it rather annoying since it didn't fix ANY flaws of the original, like the lack of fucking speed up function. I also feel like it focuses a bit too much on heroes and special events than on actual tower building and blasting shit with them.
http://www.kongregate.com/games/StormAlligator/demons-vs-fairyland - basically a clone of Kingdoms Rush, nothing special but if I'm not mistaken tower placement is slightly more strategic since you need to build barracks before building towers, or something. I suspect its shit.
http://www.kongregate.com/games/booblycCom/incursion - another clone, this one feels a bit better, it also puts more units on the map, not only soldiers that block enemies. You can also mix soldiers from what I remember. There is also a sequel to it.
https://itunes.apple.com/us/app/kingdom-rush-origins-hd/id904737541?mt=8&ign-mpt=uo=4 - second sequel to Kingdoms Rush, sadly only on phones. Probably more of the same, again.
Original is also available on Steam if someone wants to pay money for it.
Sky Island:
http://www.kongregate.com/games/Neutronized/sky-island - puzzle platformer with a twist, basically 3D game in 2D environment where you need to change your position in order to see other parts of the object. Towards the end it can get rather annoying but I don't remember any other game doing something similar so its an interesting experience.
Morningstar:
http://www.kongregate.com/games/RedHerringLabs/morningstar - this was mentioned earlier in the thread if I'm not mistaken, but I bring it up since a "remake" with added content and better production values was released recently -
http://www.postudios.com/company/games/morningstar/index.php
Sushi Cat 2:
http://www.kongregate.com/games/ArmorGames/sushi-cat-2 - you like sushi and cats? Play this game and shut up.
Alice is Dead:
http://www.kongregate.com/games/ImpendingRiot/alice-is-dead-ep-1 - three parts adventure game. Third part seams to be coded badly and has noticeable lag. I like it because its basically a reimagining of well known tale, it can get creepy at times too. It seams that were was supposed to be a fourth part, but sadly it wasn't made, for some reasons.
Hood:
http://www.kongregate.com/games/Hyptosis/hood-episode-1 - another reimagining by same guy as Alice is Dead. Same as above basically, main attraction is a spin on a tale that everyone knows.