Linda³ Again- I know it was only translated somewhat recently, but I absolutely could not put it down despite its rudimentary combat system. The Space Ark premise was intriguing right off of the bat, the characters and dialogue are charming, its open-endedness reminds me of Majora's Mask or Fallout in some ways where as time moves forward you see towns get progressively more deserted as the populace evacuates the planet. That's not even mentioning the batshit crazy creature designs or the progressively more batshit crazy and memorable plot that will stick with you for awhile. The official art for the game is very stunning. Really a one of a kind game that blew me away.
Run Saber - one of those quick and dirty arcade action games that you can finish in probably an hour. Only 5 levels but they're all pretty interesting, as is the bestiary. It's just so much fun to pilot the two main characters. Laser swords, wall jumps / climbs, ceiling climbs, slides, dive kicks and even a Samus-like Screw Attack. I've 1CC'd the game several times.
Kick Master- I loved it for many of the same reasons as Run Saber, the main character is just fun to use. I never expected such a robust moveset out of an obscure NES game. It had some pretty nice spritework from what I can recall, as well.
Arc Rise Fantasia- don't know if the Wii still counts as 'retro', but this JRPG flies under most people's radar in my experience, mostly due to its laughable dub. It's got one of the most solid combat systems out of any JRPG I've ever played and is easily one of my top 5 JRPGs of all time. The boss battles are really memorable and demand a lot out of you- since your entire party shares Action Points you have to manage your actions carefully or get stomped. I could go on and on about it. Really surprised me for what initially seems like a low-rent, turn-based Tales clone.