Here are some products that are not well known, but are amongst the finest products that I have seen recently:
Testament: Biblical RPG by Green Ronin, incredible reading and many different styles of play available. Possibly the best d20 product ever, even more than Mutants & Masterminds, and that isn't something I say lightly.
Skull & Bones: Pirates, Green Ronin style. All you could ever want to know about pirates, voodoo, ships, and the lives of the desperate in the Carribean. Green Ronin is definitely the company to watch.
Grimm: d20 in the world of children's fairy tales turned sick and twisted. Very innovative stuff.
Deathstalkers: A couple of years old, but a great and massive dark fantasy RPG that does things with combat systems that would make other games shake in their boots. Mostly easy system (non d20) with incredible maps and storyline.
Okay, those are just a few I can think of right now. I'll add some more later. Basically, I want to let people know about some of the more awesome games out there that aren't as well known as they should be because they are not backed by White Wolf or WotC.
If anybody out there has any personal faves that are not household names but should be, let me know. I'm always on the lookout for something new and innovative, even if we never actually play it.