Ummm...do crossovers count? This site covers Super Smash Bros. so...
I use RPG Maker XP a lot, mostly to make weird crossover games.
Several of them, but none are complete. (if I spent more time on one, instead of less time on many, maybe I would have finished something!) But...there is one character I put in more of my crossovers than any other. That character would be Samus! There's just...no substitute.
And I should say that my crossovers use official artwork from games. So...some of the pictures I use are from here, just saying. I of course, plan to give credit. I couldn't do it if weren't for sites like this.
Anyway. I have 4 crossover RPGs with Samus, and 2 more that she will appear in!
Don't get excited or anything, none of these are anywhere near completion.
(oh, and I KNOW the screenshots aren't very good. The pictures aren't even scaled very well, but they are the best I can get at the moment...)
CROSSOVERS WITH SAMUS
1. A Nintendo crossover where you pick a team of Nintendo characters to take on Bowser's Castle, it's a "dungeon crawler". Samus is one of the selectable characters, and I considered making a Metroid playable as well.

2. A fairly simple crossover with all kinds of weird stuff, like Donatello helping Princess Peach fight Bowser. But Samus is one of the playable characters, she helps Sailor Venus save Donatello and Bridget from Vile early in the game.
3. A weirder crossover with an unlikely team of villains causing all sorts of trouble. Who can stop the schemes of Ridley, King DeDeDe, Shredder, and Team Galactic? Well, Samus for one. Samus is introduced when Kagome is warped to Tallon IV, where Samus helps her try to find her way home, but Tallon IV isn't the same as it used to be. Samus will have her Varia, Gravity, Phazon, and Zero suits in this game.
4. A crossover that was planned to "Simply" be a crossover involving Mega Man X2, Skies of Arcadia, King of Fighters XI, and Chrono Trigger. Instead...you pick a team of 3 (you pick a whole team, no mixing and matching) to take on RPG versions of all the levels from Mega Man X2. But Samus, she's so awesome she goes it solo. So, in this game she's not balanced with the other characters, but she doesn't get back-up.

CROSSOVERS THAT WILL HAVE SAMUS
1. My first, biggest, most ridiculous crossover will have Samus. At some point in the game, you'll travel deep through space. Samus will be one of your best allies at this point.
2. A crossover set mainly in space. The main characters are slightly villainous, but Samus helps them out for some reason, maybe to set them straight. She will have only the Fusion Suit in this game.
I also have several game IDEAS that would have Samus in them. But those are just ideas, the above 6 are all started projects.
AND........
My current project...won't have Samus. But it will have Phazon as an important part of the story. The main antagonists are combining Phazon with other powerful, dangerous materials to create something horrifyingly powerful. They are so evil, the Space-Pirates form a (temporary) truce with you to stop them! A Space-Pirate or [something]-Trooper will join and assist you. (maybe an Ice Trooper, gotta represent!)
I just love Metroid enemy art, and I always find a way to include something in my crossovers.
Are these games exciting? Probably not. Are they anywhere near done? No way. Do they accurately represent the characters? I don't know, but I try. Will they probably turn out lame if I ever finish them? It's possible. Will I ever finish all of them? I doubt it. But do I have fun making them? Certainly! And I think at least someone else might too...