I've already mentioned this before, but now I'm going to go into detail on the topic of independent games. As much as I like some of the mainstream stuff, there's a fair share of games made by smaller companies (Grasshopper Manufacture, G.Rev, Wayforward Interactive, etc.) that depending on the situation; get noticed or left behind. After reading Egoraptor's review of Braid for X-Box Live; I decided to do something similar to other little-known games.

1. Rosenkreuz Stilette (German for "Rose-Crossed")
When compared to Mario clones, Mega Man clones are few and far between. Then came a company called ERKA:ES with this game which combines Mega Man gameplay, CastleVania Aesthetics, and Germanic themes (as in most of the game's characters have German names). You play as Spiritia Rosenberg, a magical girl with a different wardrobe than most, to stop Count Michael Sepperin and his daughter Iris.
2. No More Heroes
This may be somewhat of a mainstream game, but damn it, it's a blast to play. Sure, there's GTA 4, but the concept behind that has been run into the ground by now.
3. Cho Aniki Mura
Ghosts 'n Goblins meets the homoerotic space shooter Cho Aniki (Japanese for "Super Big Brother"), with a ninja who resembles Naruto's Kakashi.
4. Thunder Force 6
It took forever, but at least Technosoft let Sega work on it. Thunder Force started in 1983 as a free-roaming Xevious-clone, and was then followed by three Sega Genesis sequels. The last official release of the series was first released on the Sega Saturn, and then followed by the PS port in 1998. Then there's Broken Thunder, but that was incomplete when that was released.
5. Kamui
This can be summed up as a Rayforce clone with some pretty inventive boss fights of any vertical shooter out there. Rather than move your ship's reticle over the enemies on the ground, you hold down the thunder key (X is the default) then release when you have enough energy. Unlike most shooters, you have both a lifebar and ship stock. However, even on easy, you will still get plastered by enemy fire if you aren't careful.
6. Ether Vapor
Ether Vapor can be summed up as Axelay with more perspectives and plot development (even though there's no English translation at the moment). Not to mention it's the only space shooter with gamepad stick support.
7. Es
Here's one game that's intense, fun-looking, and also cool-looking. I can't wait for the completed version.

There are lots more out there, but It would be impossible to cover them all.

*Note: This is nowhere near complete at the moment, but I'll continue when I can.