Don't know if I mentioned it, but Quest 64 for me, as well as its GBC demake, Quest RPG: Brian's Journey.
As for more obscure games:
* Sword of Hope (Game Boy). Also, its sequel, Sword of Hope 2, which unfortunately has some severe balance issues. (Imagine if you took an adventure game like Shadowgate, but then added RPG mechanics, with random encounters, XP-based leveling, and of course shops to buy equipment. SoH2 pushes the RPG aspect more heavily, while I think SoH1 has stronger adventure game elements.
* Centauri Alliance (Apple 2 and Commodore 64): Can be described as Bard's Tale in space. Has some interesting mechanics (including one race that can transform into various creatures, including dragons that can randomly cast powerful psionics for free), but unfortunately does have some issues. (Actually created by the one who created Bard's Tale 1 & 2, though it may have been his last RPG before he left gaming to pursue religion; also, the game came out only on platforms that were almost dead at the time.)
* Wizardry Gaiden 3 (Game Boy), 4 (SFC), and Dimguil (PSX): Japan-only releases that take the classic Wizardry 1-3+5 formula, but add races and classes introduced in Wizardry 6. These games aren't without their issues, however, but they can be fun for fans of the series. (If you play Wizardry Gaiden 4, do not use the spell that is supposed to allow the removal of cursed items, as that spell has been known to cause save corruption.)
* Wizardry 4: This may be my favorite of the classic Wizardry games. It's an adventure game disguised as an RPG. Battles play out in classic Wizardry fashion, except that you're on the enemy side. You do not level up by killing enemies, and there's no shop; your only rests are at pentagrams, where you can summon new monsters to help you. The game can be difficult, and it can be trolly some times (if you've never died from an eneny's MAKANITO spell, you haven't played Wizardry 4 enough to fairly judge the game), but it's definitely an interesting experience. One point of advice: If the game warns you about a point of no return, it's being serious, and it might be a good idea to take advantage of the fact that you get *8* save slots.