Hard To Port
There's one game that no console plays well, and that is catch-up. All systems eventually face a time when they're simply incapable of properly handling the newest and biggest games on the market. Sometimes publishers want to milk their hit title by porting it to every system imaginable, regardless of their individual capabilities; other times, they are forced to continue using an outdated system because its next generation sibling isn't ready yet. In any case, developer and consumer alike would have been better off with games designed to emphasize the strength of each system rather than shoehorning in whatever was popular at the time.
The following are just a few examples of high-end games ported to low-end systems. Feel free to add your own in the comments. Keep in mind that I'm deliberately ignoring certain games like the infamous 2600 version of Pac-Man, as its failings resulted as much from rushed production and managerial incompetence as it did technical limitations.
Double Dragon (Atari 2600)

Arcade

NES

Atari 2600
I was surprised this game existed at all; the 2600 is mostly known for simple, single-screen arcade titles, not fighters with multiple moves and characters. But by 1988 the system was eleven years old, and there was only so much they could do. With only one action button, different attacks are assigned to a button + joystick direction combination -- holding up and pressing fire does a flying kick, for instance. Since the joystick is also needed to, y'know, move around, you can often find yourself moving slightly away from your enemy and then attacking the air. The problem is exacerbated by stiff controls and enemies who suffer none of these hindrances, meaning they can bludgeon you to death while you're wiggling around trying to do a kick.
One must admire the effort, though: There are one and two player modes (though in the latter each player is restricted to either the top or bottom half of the screen), and even a two player versus mode. They've included weapons, even if that just means a brown rectangle (bat) and white rectangle (knife). Linda and Abobo are here too, albeit with Linda looking like a strip of cabbage dipped in mayonnaise.

Even some of the music made the transition, though after about 5 seconds you wish that it hadn't.
NES Stage 1 theme
Atari 2600 Stage 1 theme
And it just goes on like that.
Zaxxon (Atari 2600)

Arcade

Colecovision

Atari 2600
Okay, I admit, this whole article could just be about the 2600 and its many ill-advised arcade ports. But while many were simply clunky or ugly, a select few make you wonder why they ever thought it was a good idea to begin with.
Zaxxon and isometric perspective are inextricably linked. If a person can't remember anything else about the game, they at least remember that. For a while, if someone wasn't familiar with the term "isometric perspective", you could just follow it up with "Y'know, like Zaxxon." It's the element that really made the game stand out in arcades, next to the comparatively flat and simple likes of Burgertime and Dig Dug. Thus it was only natural for the developers to completely remove the single defining aspect of the game for a port to a system that shouldn't be attempting this kind of game anyway.
Though, like Double Dragon, you do have to give them points for trying. They replaced the 3/4 view with an equally unusual heads-on perspective, with barriers and enemy sprites moving directly towards the screen. It's not exactly Space Harrier, but it at least allows for a vague approximation of the original's gameplay. Unfortunately, the missiles are gone (aside from the one on the robot's shoulder) and while the altimeter is still present, it's pretty much impossible to tell the height of anything on the field anyway. For reasons unknown, the altimeter is removed for the space sections and you fight on a single axis.
While the Zaxxon name should never have graced the 2600, I can't help but think something could have been made of this game with more tweaking and without the standard of the arcade title to live up to. Maybe drop the space bit and turn it into River Raid 3D.
Rise of the Robots (Game Gear)
DOS

SNES
(The Game Gear shot is tiny to maintain native resolution, but you can click to enlarge.)
It can be hard to tell when a port is bad when the original game was terrible anyway, but the Game Gear edition of Rise of the Robots does what it can to let you know. The one selling point Robots had (and it wasn't much of one) was its rendered characters and fluid animation, and while they did manage to keep some of the FMV for the Game Gear port, the rest of the game is a mess. Sprites are small and ugly, the animation is choppy, and the blue blob and yellow chunk are fighting in front of what I can only assume is a giant Twizzler. But hey, maybe it will get better with the next fight.

nope
I also want to point out that in the process of taking these screenshots I killed the yellow metal thing by continually kicking it in the toes until it fell down, but the timer keeps going during the death animation. So after it hit the ground the timer ran out and the game declared the round a draw. Rise of the Robots sucks.
Virtua Fighter 2 (Genesis)

Arcade

Saturn

Genesis
{arcade shot borrowed from KLOV)
One way to get around the fact that your system couldn't possibly handle the game in question is to turn it into a completely different game. Wanting to combine the popularity of the Virtua Fighter series with the popularity of a Sega system more than five people owned, Sega decided to squeeze their next generation, made-for-the-Saturn arcade fighter onto the last generation, totally-not-a-Saturn Genesis. The change is so drastic that one could argue it doesn't even count as a port, but what else can you call it? It has the same name, look, characters, and moves, the only thing that's missing is everything that drew people to VF in the first place.
What's odd about the port is that even after taking the 3D out, they still couldn't seem to make the game work on the Genesis. They also had to remove Shun and Lion from the character roster (the very two characters introduced for VF2 to begin with), cut several backgrounds and moves, and take out every game mode that wasn't arcade or versus. It makes one wonder why they bothered at all, or at the very least didn't just call it a port of the first Virtua Fighter. Yes, the obvious answer is "money," but surely they had other franchises they could more easily exploit. There's a Sonic golf game out there just waiting to be made.
Street Fighter Alpha 2 (SNES)

Arcade

PSX

SNES
It should go without saying that an arcade game made in 1996 ported to the SNES is going to lose some things in the translation. The sprites are smaller, the animation has fewer frames, the color palette is limited, the secret characters are gone, and the music is more MIDI-ish. But what's actually more notable is how much remained intact. Thanks to a special data compression chip, all the characters, stages and endings have been retained. Hell, even the intro is still in.

Arcade

SNES
While it would never be chosen over the PSX or Saturn versions, this was still a decent port if you really wanted to play Alpha 2 and all you had was a Super NES. The major issue against it is not the drop in resolution but in speed. Even at the highest speed setting, the game feels muddy and clunky. Not enough to completely ruin the game, but enough to remind you you should really be playing this on a more well-equipped system.
Trivia to pull out at your next cocktail party: Due to the aforementioned data compression, Street Fighter Alpha 2 is on the shortlist of SNES games that have noticeable load times. It's not on the level of a CD game, but it is a few seconds worth, and not at the greatest of times either. The game pauses for a few seconds after "Fight!" has appeared on the screen, meaning you've got to start moving as soon as the pause is over, without knowing precisely when that will be.
SimCity 2000 (SNES)
DOS

Super NES
The original SimCity was a welcome surprise early in the life of the SNES; it was the kind of game rarely seen outside the realm of PCs. When SimCity 2000 hit DOS a couple years later, people naturally wanted to bring the sequel over too. Whether this was a good idea remains a matter for debate.
This is indeed SimCity 2000, with all the same gameplay and features, including the ability to query individual buildings and read the local newspapers. They even added a couple little touches, like seeing rain and snow, and the shadows of clouds passing by on overcast days. It's certainly an accomplishment, but the trade-off is that the game chugs. Loading a map takes 15 to 20 seconds, and from there pretty much anything that involves redrawing the map requires a two-second pause. Re-center the screen, wait two seconds. Go to the map screen, wait two seconds. Leave, wait two seconds. It may not sound like much, but given that the game has only two zoom levels -- the third, farthest out zoom is gone -- you have to move around a lot, and the game's sputtering engine could irritate you after too many hours of play.
That said, the original DOS version was never exactly a hot rod to begin with, especially on lower-end systems. So maybe you can come to terms with the speed. Then all you're left with is the fact that the game is kinda ugly, with pixelated buildings blending into one another and making it harder to pick out individual locations. Like SFA2, it's certainly nothing you would have chosen over the original, but if a Super Nintendo was all you had, you may have been able to bear with its faults (and its occasionally questionable text) and just be happy you were getting a chance to play SimCity 2000 at all.
The one unforgivable sin: No mouse support. Ick.

Comments
I remember renting SFA2 for my SNES and being utterly confused when the game froze after FIGHT! was declared. I couldn't wrap my head around there being load times.
I was really surprised, however, at just how good of a port that it was.
Posted by: Jim | September 10, 2007 7:26 PM
I've pointed this out to you before, but it's worth mentioning that the GameBoy port of Mortal Kombat ranks among the worst games I've ever played. The animation was so slow that an uppercut took longer to execute than for an opponent to thaw from Sub-Zero's freeze. Even if the move was executed properly (and that was a challenge in itself), the AI would thaw out and wander off while your laborious slow-motion swing was hardly at navel-height. There's only one combo in the entire game, and they managed to fuck it up.
Posted by: Sarchasm | September 11, 2007 8:06 PM
NeoGAF has a thread about awful ports that was spotlighted on BoingBoing's new Gadgets blog recently. I'd find the post but I'm on my Wii right now, just search for it at gadgets.boingboing.net. I posted a link in the comments to a vid (found via Racketboy) of Street Fighter II on the Turbografx16 as an example of a surprisingly excellent port.
Posted by: A New Challenger | September 12, 2007 1:56 AM
you forgot half of the wii's catalogue lol
Posted by: webber | September 26, 2007 4:03 AM
I actually thought Zaxxon was pretty good on the atari as a kid, but I wasn't an arcade gamer, so I didn't know there was any precedent for it to play differently. It was tough as heck though, but so were most atari games.
Posted by: Mike | October 1, 2007 12:07 AM