Well, considering aesthetics, challenge, uniqueness, dialogue, et al, I would have to say that some of my favourites would include:
Earthbound, for art, humour, and general uniqueness: Seriously, who ever would have thought that in a genre conquered by the idea that all action must take place in a more primitive age, or a completely fictional one, that an RPG storyline could exist in an environment so eerily similar to ours? Seriously, there is tons of intrigue in the story of the boy who was destined to pick up his baseball bat and smash some aliens back to their own dimension. Having the cell phone on which your dad or random friends would call you on was also priceless, and, of course, the ability to erase giant pencil-shaped statues which block your path for whatever reason other than that's how the game works. Seriously, there is never a dull moment here.
Super Mario RPG, for taking full advantage of three axes of direction, and just being damn funny: In all fairness, having random characters and a storyline that detracted from the rest of the Mario storyline was sort of odd to get used to, but as soon as I had gotten into the humourous bits and pieces (even being reduced to reading monster's minds) and even strange stories being told in the middle of battles, I knew that this was a fine RPG, even though I only played it when I was, well, eight or something.
Shin Megami Tensei Nocturne, for being the most visually-enthralling RPG, having the most amazing combat system, and for proving that your character doesn't always have to be the hero...: If you have never heard of this PS2 RPG, then I strongly suggest that you go out and give it a try ASAP. This RPG completely changed the way I had originally thought of RPGs, complete with post-apocalyptic storyline, dark with flashes of humour, gorgeous graphics, and an amazing orchestral soundrack complete with the most hard-rocking electric guitars ever present in an RPG. Basically, your character is trapped in a post-apocalyptic Japan that has litterally curled up into a ball and sealed itself off from the rest of the world, thanks to a powerful magic that also killed many other occupants, save yourself and a few people whom you know. Eventually, the story turns to who is going to rule in this new desolate land, populated by spirits and even dark forces who slowly turn everyone you know into demons, and eventually climaxes with the question of whom you must follow in this destroyed world, or if you should just kill them all and conquer the wasteland yourself. In any case, it is an amazing storyline in which you slowly watch as otherwise normal people lose what is left of their grip on humanity and become twisted monsters bent on imposing their wills on what is left of their home. The battle system also rules, as your character can recruit enemy demons to work for him in the middle of combat, and eventually learns how to fuse them into a single, more powerful entity. Any monster in the entire game is available to you, with the very last boss being the only exception, and you can create a party fit for any situation, improving on it and changing it as necessary as the game goes on. Finally, Dante from Capcom's Devil May Cry also appears in this game, and often tries to kill you but can eventually be recruited as a powerful ally. Go out and play this game, you will not regret it.
Shin Megami Tensei DDS, for being the most difficult to complete, and being the most satisfying as well: Despite having the same title as the aforementioned Nocturne, DDS has a completely different storyline from its predecessor, and the only things linking it to Nocturne are probably its graphics, elements of its battle system, and its electric guitar-backed orchestra. DDS, however, is far more challenging to complete, as its battle system, while similar to Nocturne's, gives tougher penalties and greater rewards to those who can exploit all its nuances. Basically, if you can successfully exploit an enemy's weakness, you get more chances to attack him for subsequently greater damage, but if your attack is blocked or dodged, you lose turns and your enemy gets to counterattack more quickly. I am not kidding when I say that in the late stages of the game, one otherwise minor slip-up will result in your entire party being annihilated in a few turns. Expect to die quite often if you play this, but take heart in the fact that most of the levels in the game have an abundant number of save points, most of which will also heal you for a small sum of money.
These are some of my favourites, and I highly reccommend them if you haven't tried them already.