My vote for best anime/manga based PCE game is . . .

[Naniyue]

Wataru/Keith Courage is a disappointment.
I love the Macross games! One is a shooter, the other a tactical RPG from the makers of Langlisser!
I haven't played all of the digital comics yet, but the Ranma 1/2 and second Devil Hunter Youko ones were fun, and Sailor Moon was okay.  I haven't played Yuu Yuu Hakushou, either.
Cyber City OEDO is kinda boring, but the anime was good.  I liked the first Lodoss game, even if its system wasn't perfect.  3x3 Eyes was pretty good, and way better than the PC98 version.

Ultimately though, it would have to be . . . Yamato!

  The cut scenes, the game play, the tension.   It really feels like you are a part of the anime!  Play through highlights of the original series!  If you are a Starblazers fan, you won't even need to know Japanese, except for the cardinal directions near the end.

[Necromancer]

I've played a couple of those mentioned (Keith, Sailor Moon, and 3x3 Eyes), as well as the Yawara pair, Lum, Tenchi Muyo, and the Yunas.  They were all good fun but nothing that'll land on anyone's top 10 list.

My favorites would have to be Cosmic Fantasy, Ys, and Castlevania, but they're backwards - anime made from games.   

[Naniyue]

Cosmic Fantasy is my favorite 16-bit JRPG series.  The character designs can look silly one moment, and then dead serious the next.  I did watch the anime a couple years ago.  It was OK.

[Necromancer]

Did you watch it with superdeadite's translation?  That's a big part of why I enjoyed watching it.   

[Naniyue]

I don't remember, but it was a decent watch, regardless.

If you enjoyed 3x3 Eyes, the Yunas, and all that, I do suggest playing the second Devil Hunter Youko game.  It takes place where the first one left off, but the first one was such a boring chore, I suggest skipping it.

  All three Ranma games have great cut scenes, but game quality varies.  I swear the first is impossible to beat without cheating.  The second is like the Yunas and I found it amusing.  The third is a mediocre fighting game, but it wasn't too bad.

  Anyone tried the Yuu Yuu Hakushou one?  I'm not a fan of the show, but I'm still willing to give it a try.

[Necromancer]

I'll add the Devil Hunter pair to my list of stuff to try to beat.  As a retard, I can't outright skip the first game...

[majors]

I enjoy anime but haven't played a lot of "anime" games for obey due to language barrier. However, I did enjoy Private Eye Dol's recent fan translation. I'd considerate it to be "anime AF". I also recall playing Future Boy Conan decades ago and beating it. Since it's a platformer, it plays easy enough for a non-Japanese speaker.

I played Cobra on Sega CD b/c it's in English, but it also is on PCE. I'm not the biggest fan of digital comics but I did finish it.

YuYu is on my short list to get for PCE. I've emulated it, and it's seems pretty simple and not much meat there, hence it sells for $10-20. Reminds me of Operation Wolf.

[Androsynth]

My vote goes for Macross: Eternal Love Song. Not only is it a stellar turn based RPG with all the cool mechs and ships from the show, it's a direct sequel to the movie retelling 'Macross Do You Remember Love' which is basically it's own timeline. The events of the game are the only known sequel to that retelling (which was later absorbed into canon by making it the 'in universe' movie telling of the events of the original series), adding to the interest.

But honestly, it's just a damn good game by the same devs who made Langrisser.

[Naniyue]

As a Robotech/Macross fan, I agree that Eternal Love Song is an AWESOME game.  I just think Yamato has better presentation, but ELS is definitely better in the gameplay department.