A buddy of mine asked and all I had handy was Super Cosplay War Ultra… which is pretty dated. The other good ones I know of now have mainstream ports.
So… what don’t I know? One or two will be fine.
Super Real Bout 2: The New Challengers (J)|
Oh, and Akatsuki Blitzkampf. Actually the best doujin fighter ever. Better than most mainstream games.
Party’s Breaker: The Queen of Heart 2001
Eternal Fighter Zero
Gleam of Force
Hmm, if you want something that get played that has actual tournaments I will have to tell you Melty Blood and Arcana Heart are the biggest doujin fighters in the US. Akatsuki Blitzkampf also has a pretty big scene online and offline, although it doesn’t have offline tourneys as often as MB or AH.
Queen of Hearts 2k1: Party Breaker’s, Eternal Fighter Zero, Acceleration of Suguri EX (Although I personally wouldn’t call it a fighter still pretty fun), Fuuka Taisen, Immaterial and Missing Power, and any Fate/ game are something to look out for. I would suggest Scarlet Weather Rhapsody, but I hear bad things about that game.
Let’s play ‘find the mistake’.
Arcana Heart isn’t doujin made. It’s made by Yuki.
Melty Blood Re-act and before were doujin made. After plans of MB:AC being an arcade game, i think it became mass produced by a non-doujin company or something? Unless French Bread just did a hell of a job…
IMO good doujin games:
Blitzkampf (tho like MB, it got an arcade release, and new characters, so im not quite sure it still remained a “doujin” game)
Immaterial and Missing Power
Eternal Fighter Zero
Queen of Hearts 2k1: Party’s Breaker
Around 2006 Ecole took the major role in the game, they’re the ones responsible for the arcade and console releases then.
Thanks for the explanation. I knew it was something like that. Prolly a similar thing with Akatsuki too, i would imagine…
Thank you to all who posted. I’ll be sending my buddy this list along with my suggestions for non-fighters (Crazy Power Disc, Warning Forever, etc. etc.)
Crazy Power Disc is awesome 
Too bad, I was never able to get a hold of Crazy Power Disc Perfect, the version with some extra characters.
I agree with the rest, Akatsuki Blitzkampf is the way to go.
There’s also that BigBang Beat that’s pretty and quite proffesional in quality, but from what I hear it’s quite broken balancewise.
The full Fuuka Taisen was released? I’ve only played a demo… Did Shizuru make it into the rooster? She is all kinds of awesome in Mai Hime.
Gleam of force.
Amazing game needs more love.
Nah, Subtle braught the game into the arcades on its own.If I remember correctly nobody supported them.
Imo Akatsuki Blitzkampf is the best doujin fighter and 2nd is IAMP
Eternal Fighter Zero and IaMP, maybe Akatsuki if you’re into older SNK style games. Everything else is more or less negligible.
It seems like the top games mentioned thus far are (in order of seeming support):
Akatsuki Blitzkampf
Eternal Fighter Zero
Immaterial and Missing Power (IaMP)
Gleam of Force/Queen of Hearts 2k1: Party’s Breaker
Must-have titles:
Melty Blood Act-Cadenza (not really a Doujin anymore, but it was in the beginning)
Akatsuki Blitzkampf (same here)
Eternal Fighter Zero (at least for me, the most underrated fighting game ever with Breakers Revenge)
Inmaterial and Missing Power
Gleam of Force (not really a “fighting game”, more like a boxing game, but still awesome)
Another not so good titles but i recommend to take a look anyway:
Fatal/Fake (excellent game until you find the infinites and glitches)
Fuuka Taisen (broken as hell, but not bad)
Hinokakera Fragment-Eclipse (also broken but funny game)
Scarlet Weather Rhapsody (seems that the game is inferior to IAMP, see their official SRK thread for more info)
Big Bang Beat (it started as one of the most ambitious Doujin fighting games ever but NRF screw the game with their patches and never fixed the problems. They are now making another promising Doujin title named Million Knights Vermillion).
Just for the lulz titles:
Super Cosplay Wars Ultra
Crucis Fatal+Fake (yeah, i admit it, Lights fuck up this game)
Queen of Hearts 2001 (takes the word “broken” to another dimension)
AND HOW I CAN FORGET TEH ARCANA HEARTS!!!1111 (stop calling it a Doujin game, please)
Blitzkampf of course, such a great game.
Lots of people will say Blitz is great but not actually play it. 
Brandino, dude, you know I respect you but there is nothing correct in any of the sentences you posted here.
If you are actually interested in Blitzkampf, stop by #akatsuki @ mizuumi.net on IRC. I’m always willing to try netplay as long as you aren’t on Zanzibar Coast or something ridiculous. </mandatory plug>