Well, I suppose I can tell you a little bit about good indie systems, but you'll have to take it with a grain of salt, as these are only my favourites and tastes can vary. Furthermore, I do like mechanics which emphasize the mood and setting of the game. Like for example the exalted virtue and great curse mechanic (which is done poorly, but its the kind of mechanic I like). That means I will always prefer a specialized game over a toolbox game, because toolboxes frankly suck at specialized mechanics.
So, that being out of the way, let's start with my favourite game. It is called spirits of the century and it is being done by the gentlemen of evil hat games (
http://www.evilhat.com/home/?page_id=103 ). It is the emulation of the good 1920s pulp, we are speaking of an alternate history in which the century club supports extraordinary individuals (centurions) in their battles against evil foes. If you like movies like shadow, indiana jones, the mummy or even league of extraordinary gentlemen, then you will feel right at home here. The system is not as rules heavy as exalted but it definitely has enough meat to satisfy your average crunch lover. The core mechanic is not very difficult, throw a couple of dice, add skill, compare to target number -> succeed if you at least meet, fail if not. The system operates without hitpoints or other surrogates (*cough* motes *cough*) and gives the players a couple of nice ways to influence the story in a meaningful way. Everything is written with great care and you will have a guaranteed "why didn't anyone think of that earlier, this is so awesome" moment every 3 pages (or more). If you are into pulp, then check it out. (for those who like harry dresden, the guys at evil hat are doing the dresden files rpg right now).
Next one is reign, you can find the game at
www.gregstolze.com and yes, we are talking about THE greg stolze right now. The same guy who did unknown armies, a good chunk of the excellent vampire the requiem books and other pearls. He wrote a fantasy game, but it is fantasy done right. The rules are fast, generate complex results and that without being complicated. The setting is fun and lovingly written. It is not as full of half gods as exalted though, it is more on par with all those kitchen sink fantasy series ("swords of..." for example). The author has a ton of free material on his homepage, too and is REALLY helpful.
These are my favourites, but there are many more which I adore, like for example "cold city" (mulitnational groups of agents hunt nazi experiments in cold war berlin).