So I'm not interested in posting on all those RPG's you already know about. Yes Final Fantasy 2 was awesome, and so was Final Fantasy 3. No contest. Chrono Trigger and Secret of Mana? Unparalleled. No, I'm going to post about games you might not have heard about in hopes that you will go investigate them. These are still fun and very worthwhile stories.
First up is the brightest gem of the bunch and the most often passed over by those who want a shiny package. It has a touching story, better jokes and narrative, and great puzzles nad gameplay, topped with decent although not stunning (usually) graphics. I give you Lufia 2! Yeah its ok if you never heard of it. But you've heard of it now and you should go check it out because this game is wonderful packed in wonderfulness. I particularly like the new characters added to the plot that you aren't expecting like Dekar who is beautifully oblivious to his everything (death, danger, destruction) except his own awesomeness. The improved "Old Cave" is also in this game which allows you to run a dungeon that changes each time and has changing treasures, but if you get any blue box treasures you get to keep those ones. You also start at level 1 each time you enter it, though you level a lot faster than you do in the normal game for some reason.
While I'm at it, I'll tentatively recommend Lufia 1, but only to those stalwart souls willing to play a much harder, older, much less ADD friendly game. The storyline is fantastic but the graphics totally suck. The music is pretty good at some places but annoying in others. The ending is very touching. For both games and they tie into each other well. Start with Lufia 2 as it is actually the prequel to Lufia 1 anyways story-wise.
Next on the list is Earthbound or EVO I can't decide so they are both next! EVO is about evolving into something better and eating everything that stands in your way. Eventually you get to the end and have to fight some nasty alien thing that is working with other aliens trying to do... something I have no idea so I can't ruin it for you. Then the Spirit of the Earth itself gives you a kiss and its happily ever after. Play the game. Its very inventive and fun whether you believe in evolution or not. You get to make your own dinosaur, and this came out eons before Spore I might add.
Earthbound is about a kid, and his girlfriend, and a geeky genius kid who has no relation to either of them initially, and a kung-fu kid who lives in an awesome city in the clouds. And a lot of very varied environments and the invasion of many aliens into each one. (Both overtly and covertly)
A very humorous British game and very creative. Not your typical run-of-the-mill game. Expect to be weirded out and amazed.
Secret of Evermore (and Final Fantasy 5 If you are brave)
Secret of Evermore is a very hard game. It says Squaresoft but it was developed by a U.S. company contractor. The dialogue, plot devices, gameplay, everything is very different, except the real time combat feels a bit like Secret of Mana. You use components to cast spells on your foes with alchemy. You are in a fictitious world called Evermore which grants each person in it their utmost desires, which can really be a problem when there's nothing to oppose them, so it generates its own evil to oppose them too. you have to find a way to destroy the world and get the normal people in it back to the real world. Your dog can change into a cave-dog or a toaster dog or a poodle or whatnot. Lots of fun.
Final Fantasy 5 I hesitantly recommend this one for you junkies out there but be warned, this final fantasy is actually hard and really really really long. and Really grindy. You WILL have to go "gain 10 levels by killing feral chocobos" before you're allowed to beat the next boss or whatever. Still the plot is unique and neat and involves an evil being who, as usual, wants to destroy everything but this time he wants to suck you into a dimensional vortex where the world you explored is all mish mashed up, pretty interesting and long final level.
Ok no more square games: next up is Tales of Phantasia. Side Scrolling, monster slashing, totally unconventional combat system for the time and good plot to boot. This wasn't released on the Game boy advance until 2006 so you can go pick it up in the used games store still I bet. Tales of Symphonia is a beautiful game for the Wii. I haven't tried the second one yet though so I can't recommend it. Anton hates the combat though I think or something about it. I and all my bros loved the combat but we hated the camera. (It's 4 player at the same time but the camera is always on the lead dude) It's always something right?
Fire Emblem (get the GameCube one, it has the best story) This game is turn based strategy where if anyone dies, they stay dead. That goes for your enemies too, none of this: "just kidding I wasn't really dead" crap we get from Squaresoft and Blizzard all the time.
The story is well done and changes a bit depending on who survives. Along with that you get some choices that influence the plot in your conversations in and outside battle.
If you want a farming sim/rpg go to Harvest Moon, though I didn't like the first one as much as later ones.