My biggest one would be Xenoblade Chronicles.
Where do I begin? There was this whole huge movement called "Operation Rainfall" to get this game and two other games translated and dubbed for english audiences. While I can't say I've played the other two, I can say that I have no idea why people wanted this game over here because the plot is cliche, stupid, and wastes potential, the gameplay is repetitive, has zero variety and is incredibly grindy and at times, unfairly cheap (why is it that I can't beat a bonus boss that my entire team is five levels above?), and while the presentation is some of the best the Wii has to offer, it still doesn't measure up to HD console games, and sometimes causes slowdown issues. I just don't understand why people love this game, I don't...

Davideo7 : Alright, it works fine on Firefox, though I haven't tried to record anything yet. I probably should have mentioned that when I was using IE, I was getting audio just fine; it was just the visuals were stuck on the loading screen.

On top of that, the audio lags while I'm playing the game itself when using Mednafen, though it may just be because I haven't installed the optional plugin yet.

Davideo7 : I'm using Internet Explorer on Windows 7. Should I try again on Firefox or Chrome?

Davideo7 : It doesn't matter the game; all the GBA games get stuck on the loading screen when I try playing on Medafen. I tried changing my computer's resoultion, but that didn't help either.

Of course I have a superpower. I can make water instantly boil! Kinda gruesome when you use it on a person; it's like half of them instantly vaporizes, and then you get this pile of internal organs and bones... Great for instant noodles, though! You may call me THE AMAZING STEAM PUNK! HA. HAHAHA. HA.

Can't beat Clank when it comes to sidekicks. Dude's a genius, can command small armies of robots, assist in acrobatics and swimming, is compatible with many different types of machines, can turn into a giant and destroy small planets, and also stars in his own TV show. He's got it all. Just make sure he doesn't get infected with a Missingno glitch; those can be annoying.

Runner-Up would be Rush from Mega Man. Just because.

Though I don't often end up using one much, I really did take a shine to Electabuzz. It's got an awesome cry, looks cool, and has useful moves, it's just more often than not I end up using Jolteon, Manectric, Luxray or some other electric type before I get an Electabuzz.

In terms of sheer usefulness, though, that's a toughie, but it'd be somewhere between Swampert, Wailord, Snorlax, and Scizor.

I like this game, but I'd disagree that it's underrated, and especially that it's one of the greatest ever made. The series it spawned may have improved over time (wouldn't know, haven't played them), but this game really hasn't aged all that well.

For starters, you're almost never given any kind of direction. Even if you're playing the game translated, expect to be consulting guides constantly.
 
Second, the game has random battles everywhere. Seriously. There are few to no safe areas in the game, depending on what point you're at, and don't expect the safe areas to have heal points or shops. No, those are in the danger zones, which makes no sense at all.

Next, there's zero indication of what any of your spells or items will do until you actually use them. This can be a problem if you've had something useful all along, but didn't want to risk finding out whether it was useful out of fear of losing MP.

Also, you're forced to distribute stat points before you know how your characters will use them, always a problem. Your main character doesn't have any magic at all, for example, but before you know that, you can put valuable stat points into his magic stat.

And lastly, the graphics and dungeon/exploration system shows tremendous age, as you'll have to explore long hallways and buildings with no distinguishing features in complete first person, making it easy to get lost. Thankfully you do have a map, and navigating would be near impossible without it. However, there are still traps in the game which don't look any different from normal spaces and have no way in which you can detect them without walking right into them. Again, you'll have to use a guide. Worse yet, some of these traps are unavoidable. You'll have to walk over them, violating common sense.

I will say that the game did introduce a ton of good ideas, and other than the above, is very enjoyable.

From what I've played:
1. Final Fantasy V Advance: Best class system I've ever seen in a video game, and a self-aware story that takes its clicheness and runs with it. I love this game. Played FFI-VI, and this is easily my favorite.
2. Paper Mario The Thousand Year Door: This is the only Paper Mario game I've really spent time playing, and I get the feeling it's the only one I'll need to. Unique settings, no grinding required, lots of strategies, and tons of personality. More RPGs should be made like this.
3. Mass Effect 2/3 (tie): As one of the few people who wasn't outraged over the plot of Mass Effect 3 (due to my probably somewhat lower expectations), I enjoyed both of these games equally, ME2 for its better character writing and story, and ME3 for its better gameplay. Not much I can say, that hasn't already been said.
5. Breath of Fire II: As this is the only game I've played in the series other than Dragon Quarter (which I could not get into due to the setting being terribly lifeless and dull), this gets put here. It's largely because of nostalgia, but it was a genuinely good game with a solid battle system, good music, a colourful setting, a decent plot and interesting characters. Only real complaint is how the translation team felt the need to abbreviate everything. 

I've played every Metroid game that wasn't a spinoff, and I loved them all except Other M. Couldn't really get over the bad missile control, the overly dark environments, and those stupid sections where they force you to look for something in first person and you really have no idea what it is, so good luck finding it without a game guide.

But actually, I'd rather talk about Metroid 2, since everyone seems to skip that one. I did play with a map, but that was it. I actually found it a lot of fun, despite its primitiveness. Yeah, it's short and the graphics are underdeveloped and the lava kinda prevents too much exploration, but I found ways to sequence break anyway. If there's one thing it could have used, it's more Metroid variety, but I'll chalk it up to limitations of the Gameboy. I wonder why they never brought back the Spider Ball for 2D, it was a really useful feature; much easier to use than the Space Jump, mind you. But I'd say if you're a fan, check it out. It may look like the awful NES original (which we now have Zero Mission to make obsolete), but it's much improved.