I don't have the time to list what immediately comes to mind off the top of my head, but how about these-
OVER-RATED:
Kaze-Kiri: if it were as common as Keith Courage everyone would be asking where the gameplay is. Bravoman also has a number of moves, but his game is still way better than this... -and the aesthetics are nothing special.
Shubinman III: I've mentioned before or elsewhere how underwhelmed I was with this game. I did only first try it within the last few years, but the gameplay appears non-existent, the sound jumbled & almost buggy and the visuals consist of lame art with a decent transfer.
Cosmic Fantasy 2: I liked it back in the day and still appreciate it since it is a Turbo game and WD's awful "translation" actually fits here(but nowhere else). But the game needs to have the hour-long turn-taking boss fights fixed at the very least. If I remember correctly, WD f*cked this game by "fixing" it like they "fixed" Eternal Blue. Still, this game would be in this list if everyone didn't rate it so high.
Magical Chase: it doesn't feature 256 colors onscreen(no Turbo/PCE game does) but it is a more or less a Super Deformed Lords Of Thunder. Another game few would care much about if it was packed in with the original TG16 and given a crappy american comic. Again, I still love it like pretty much all PCE/Turbo games, but its way too over rated.
Beyond Shadowgate: Now this is the KING of over rated Trurbo games. Again, it not only doesn't feature 512 or 256 simultaneous colors, it actually has only 16 colors or less in the bg's and the worst amature sprites and ugly english art around(except the bg's). Its short, side scrolling and has some of tthe worst endings of any Turbo games. Still worth playing through once as a Turbo game, but don't believe any of the crazies who tell you that it defies the specs of the system.
Sapphire: Similar to Beyond Shadowgate in crazy rumours, but is actually a good solid game, but not really great. First of all, although we here the stories less frequently now that the Internet has caught on, it does not use the processing power of the Arcade Card to push realtime 3D graphics that rivals early Playstation & Saturn games. The '3D' portions are a poor-man's DK Country. Stills looks nice enough and is moderately fun as a CD2 or SCD game. I don't know where the 18 Megs of RAM is being used though and once again, if Forgotten Worlds traded publishing places with this game, it'd just be another shhoter.
Macross 2036: Another decent shooter that was blown out of proportion more so back in the day. Take away the Macross license and we'd have never heard of it.
Air Zonk: I love it as much as anyone but the gameplay isn't very good.
UNDER-APPRECIATED:
Golden Axe: it's not the greatest game ever made nor the best port, but not nearly as bad as most people who turn it on once and condemn it after 5 minutes will tell you. And it's greatest shortcoming is the limited gameplay of the original.
Final Lap Twin: A fun arcade racer and great little RPG. The last race is still too tuff though.
Tengai Makyo Series, particularly Kabuki Den: Even if these games received the praise out side Japan as they do inside, they'd still be under rated.
Farjius Neo Metal Fantasy: Such an amazing RPG with unbelievably boss graphics. It big, fun, aesthetically great, but even with my walkthrough on GameFAQs, am I the only outside of Japan to actually play this game through?
Side Arms & Side Arms Special: One of the better(or my fav) Capcom arcade games in it's time. Afterplaying the original on MAME again the other day, it actually looks arcade superior with it's scrolling stars versus the arcade's static bg's. Plus, like Golden Axe, you get another redone arcade CD soundtrack.
Super Darius: Even though the gameplay suffers from the cut from 3 screens to one, in that you don't have much room to dodge many of the screen filling attacks, its still awesome and otherwise arcade perfect. The real kind of arcade perfect, graphics and sound(and gameplay). Also one of the best game soundtracks ever.
Strider: More so than Golden Axe, its not that bad a port. Also more so than Golden Axe, the original version was limited gameplay wise. What we do get is graphics translated from the arcade instead of the Genesis/Megadrive's simplified completely redrawn bg's. If all you care about is graphics, then I don't know why you'd get so excited about the original in the first place. But this one still looks good and plays as good as a Strider port can. Plus another classic arcade soundtrack boosted by CD.
Conan Boy Of Future: Even I haven't taken the time to play through it, but from what little I've seen it looks like a great platformer on a system severely lacking platformers.
I love the games that I seem to be taking jabs at as over-rated, and only point out potential shortcomings in such a context.