I'm currently having a blast with The Unstoppable Gorg. Love those cutscenes.

Revenge of the Titans. Frustratingly difficult but fun.

SPaZ - one of the best indie games I ever played.
Recettear - if it can be counted as indie, amazing game that masterfully smashed together RPG and shop owning sim.

Orcs Must Die is a good way to kill some time

How about Nitronic Rush

Its made by students from DigiPen
And its free

Worms:Ultimate Mayhem is a great way to kill some of time

if you like roguelikes, then i'd recommend nethack and ADOM (dunno if they are indie.. they aren't classified as genreless(or independent) but they are developed by independent people - need to check the definition of indie games lol) anyways both are epic and worth a try

The DROD (Deadly Rooms of Death) games. They are a series puzzle games that are made by Caravel Games. Tendry's Tale is a bit different since it also has RPG elements :) There are 4 games total with a 5th on its way. There's also the Architect's Edition which is an earlier version of DROD and while the graphics are lower in quality it is completely free. All the games allow you to make your own levels and use levels made by other players. I can keep going on and on so I'll let you try these games and see for yourself.

DROD Game Demos
Architect's Edition

Well, Eschalon is already suggested a few times above... so I guess I'll have to suggest something else. How about The Spirit Engine games? The 1st game was/is always free, while the 2nd game was used to be sold but it is now free. I suppose you can count the maker as an indie game maker?

http://www.thespiritengine.com/

i'd say to check out one of the Hacker games. To The Moon is also very good

Elona's another graphical roguelike that might be worth checking out.

how about some free shmups:

Like some of Kenta Cho's games. rRootage is a boss rush game with dozens of stages for four gameplay modes based off of different shmups (like Ikaruga's polarity system). Tumiki fighters has defeated ships sticking to yours, the concept was remade as Blast Works for the Wii. Those are some of the better known ones.
http://www.asahi-net.or.jp/~cs8k-cyu/index_e.html

x.x's Blue Wish and Eden series - Cave style games
http://www004.upp.so-net.ne.jp/x_xgameroom/

Warning Forever - Boss rush game where your performance influences the next boss. If you shoot off all the armor plates on the bottom first, then the next boss will have more guns and armor plates on the bottom. If you attack the sides first, then more armor plates and guns are added sticking out horizontally, etc.
http://www.hikware.com/Prod/index.html#wf

Since you have Binding of Isaac I'm assuming you have Super Meat Boy, but that's a platformer I'd recommend.

Bastion and Braid are my two favorite indie games and I'd recommend them both, but I imagine you probably have both of those too. You also said you had Limbo, which is also great.

Amnesia is probably the best horror game I've played since System Shock 2. I recommend it to anyone who thinks they enjoy horror movies or horror games.

World of Goo is another you might have, but its an interesting puzzler if you don't.

Thanks for the giveaway

A quick FYI for those interested:
Orcs Must Die is on sale on Steam for $3.74 USD for the Basic Game & $4.99 for the GOTY which includes both DLCs. The individual DLCs are also 75% off.

This is a Mid-Week Madness sale, so those prices are until Thursday Afternoon PDT

What? This looks fantastic. Thank you for this suggestion! Even though it wasn't directed toward me, it is something I would really enjoy. :)