For learning Japanese, I would suggest to play a game that has both text and voice. If there's a word you don't know, look it up in the dictionary and have it memorized (
Anki is especially good in this regard).
Elona - An odd roguelike where you try to save the world, be able to break walls without retaliation, and ride on little girls who are your pets. Supports both English and Japanese. English however does have lots of cut scenes cut.
Freemu - Contains lots of free indie games and updates frequently.
Silver Wolf - One of my favorite developer, he has made a similar engine to RPG Makers only much more beefed up. Most of his games are made in this engine and here is one in action (RPG/STG hybrid):
.
He also holds annual contests with people who makes games on the engine. The last one just ended about three weeks ago:
http://www.silversecond.com/WolfRPGEditor/Contest/Here are some commercial games you might want to check out.
Mana Khemia (PS2) - Enjoyed the battles and overall world greatly, although the battle does somewhat fall off after halfway through.
Baldr Sky Dive (PC 18+) - I personally started with this eroge to learn and while I only comprehended about half of it first time I started(interwebs, neuro implants, and insane religious priests) it was definitely a great experience. Here is a small translation I have done over video for a particular scene(SFW):
Live A Live (SNES)
Tales of Phantasia (PS1)