I could probably mention a load of shmups and doujins no one has heard of but i'll just mention a couple of under-rated old school games.
The TRPG Langrisser series which is the IP that Career Soft worked on before Growlancer and what Advanced Wars cloned its self on. Only the Megadrive version of Langrisser 1 saw a english version under the name Warsong, the rest have been unlocalised however some have been patched to English by fans (Langrisser 2 MD, Der Langrisser SNES, Langrisser 4 PS1)
Lucas Art's puzzle platformer Night Shift. This is so under the radar its crazy, especilly as its Lucas Arts, theres just 1 gameplay video on YT. Its for most of the popular 8/16 bit home computers. Basically you run a machine that makes Lucas Arts dolls, R2D2, Stormtroopers etc you have to make sure all parts of the machine is set up correctly otherwise you get rejects. But the machine called the Beast has a habit of going wrong so you have to fix it. Here is the vid of the 1st level, as you progress parts of the machine are unlocked and you get pests, it gets very hectic and difficult in later stages as you are under the clock.
Great Escape for 8 bit home computers (No idea which is the best port but I had it for the Spectrum) Its an isometric game set in a WW2 camp, you are an inmate trying to escape. Whats interesting about the game is that the camp runs a daily routine, roll call, meals, exercise, bed time and the guards all have the patterns as well. Its your job to sneak about collecting the items for what you need while not getting discovered, there area areas where you are allowed and others where you arn't. I never did beat it I should go back and play it and Land Before Time which is similar but you are on a prehistoric island
I've just found an updated version of it called Prisoner of War PC/PS2, no idea if it's any good.
Love-de-Lic's Moon RPG Remix Adventure for the PS1 seems to be one of the best 2D JRPGs never to make it to english http://www.hardcoregaming101.net/lovedelic/lovedelic.htm