Updated to include down to #14:

16 - N64 - Banjo Tooie (Nintendo)
15 - GC   - Star Wars Rogue Leader: Rogue Squadron II (Activision)
14 - Wii  - Metroid Prime 3: Corruption (Nintendo)

All but 1 of the remaining 13 games in my list was published by Nintendo... of the 37 games I have listed so far, 18 were published by Nintendo (in Europe), so slightly less than half. Although I'll admit I was surprised some of them were published by Nintendo. I tend to think of Episode 1 Pod Racer as a Lucas Arts game (similarly I thought the Rogue Squadrons were Lucas Arts, but in Europe they are Activision) Also before compiling this list I believed that Goldeneye was the only Rare game I owned that was published by Nintendo, but it turns out they all were.

This isn't in my top 50, but it's definatly one of my favorite N64 games, and the best Space shooter I can think of (Except against maybe Project Sylpheed, but it's close). You could beat the game in under an hour, if you took the easiest path and got the half ass ending, but if you took a more elaborate path it's closer to an hour, hour and a half. Also with multiple paths there is incentive to replay this game.

I love the second landmaster level (on that moon that resembles Titan), and the level on the sun. I mean, you fight a Lava Monster on the sun!

This game literally had the best Boss Battles, Star Wolf was great, but I loved the Mech on the alternate second level, and I love any mega ships.

I think I'd best not voice my opinion of Lylat Wars other than to say I put it one place below MK64.

#15 Gran Turismo 5 played on PS3, released 2010

It's not the most polished, most consistent or most user friendly, but it is certainly the most ambitious racing title this gen offering incredible variety in tracks, race types and cars.

This is my most played game this gen and by far the game I have played most online. The room system works great and it's always easy to join your friends. You can make about any race you want all the way from a gruelling endurance race with heavy damage, dynamic weather and pit stops to fun arcade style team racing games with fast catch up to keep the field close together. Shuffle mode and the random generated tracks keep the game fresh. It's fun to see what devious tracks the current host has come up with.

I love the special stages in single player as well. A welcome break to the normal grind. They are over far too quickly but do a good job in show casing the variety on offer with go-karts, nascar, rally challenges and special car challenges. I also like the weekly added challenges for single player, there is always something new to do when you come back to the game.

The tracks offer great variety as well. The HD remakes of the classic tracks may not be as stunning as the real life and city tracks but they look exactly as how they originally did with a dose of heavy nostalgia.

My all time favorite track is Nurburgring Nordschleife and GT5 has by far the best rendition of it. I've probably spend as much time on that track as on all other tracks combined. You can wake me up any time to do a couple of laps. The track looks beautiful in 1080p in any light or weather condition. Racing on it feels raw, every bump is translated to the car. It's just as much fun keeping a go-kart steady at top speed steady as it is challenging to drive a perfect lap in an F1 car. It's such a exhilarating experience to drive with a couple of experienced racers, bumper to bumper without touching down the whole track. Passing is a risky affair, 1 wheel on the grass easily ends in disaster. This is racing at it's finest for me.

I've been addicted twice now to GT5. First time the psn outage managed to break my addiction. 2nd time the onslaught of excellent games this fall season. I'm sure I'll be hooked again next time I fire it up. 80% of my friend list is still playing it daily. Hopefully GT5 will continue to get the great support is has had so far. More tracks please.

List

16. The Legend of Zelda: Twilight Princess (Wii)

Here we are at number 16 and this is the first of 3 Zelda games in my list, which tells you something about how highly I regard the series. Twilight Princess is something of a divisive game though. Some people love it, and some people hate it. I love it, but that should be fairly obvious given that it appears here. As this was on the Wii it obviously features motion controls, and it's a mixed bag when it comes to their effectiveness. Aiming your bow/slingshot/etc is a joy, but the sword controls could have been better (and they eventually were bettered, but we can't talk about that game). Still, there's far more to this game than motion controls, as I found the story to be incredibly engaging, and unlike some I really enjoyed the wolf sections of the game. And then there's Midna, who is possibly the best sidekick Link will ever have.

Another mass update:

28. Shadow of the Colossus (PS2, remade in HD as part of ICO/SotC package on PS3)

This is typically held up as a prime example when people start describing games as an art form and it's pretty easy to see why. Unlike a lot of arty style media, this also had the bonus of being an entertaining game. The simple concept of a game filled with epic boss fights in a wonderfully unique environment just plain works, but the real beauty of the game comes in the subtle ways the game invokes emotional responses from the player, from the expressions on the colossi to the way Agro feels like riding a real horse.

27. Starcraft + Brood War expansion (PC, also on N64 as Starcraft 64)

Talk about unoriginal this game adding nothing new to RTS gameplay; 2 resources, 3 factions, basic RTS techs and units. It just did it all prefectly. Very few games in the genre are as amazingly polished as this one. The 3 races were incredibly well balanced and in the coming years were patched to perfection whilst they managed to incorporate a decent campaign mode into the game.

26. Chrono Trigger (SNES, also on DS, VC, PSN & PS)   

There aren't many JRPGs like this one, it really stands out in the genre as an absolute gem of a game. The characters were all interesting, the epic story felt like a true odyssey through time and with multiple paths and endings this really does still stand as one of the best games ever made. The graphics have aged pretty well too.

25. Neverwinter Nights + Expansions Shadows of Undrentide & Hordes of the Underdark (PC)

I unfortunately didn't get into Baldurs Gate when it came out, so this was my first real foray into Western RPGs. From the start I loved it. The story was brilliant starting with a plague in Neverwinter and multiple problems aflicting the city to the betrayal of the Aribeth and the way the player handles each situation. The expansions were also good adding in prestige classes as well as new stories. Played this co-op with my partner which worked very well.

24. Starcraft 2: Wings of Liberty (PC)

Sequel to the game that's a Korean national sport and has sold over 10 million copies worldwide, Starcraft 2 is just superb. Everyone knows its popular in multiplayer (although the Terrans were somewhat overpowered and the Zerg the opposite on release), but what I was suprised with was the excellent single player campaign. You can see a lot of care and effort went into building a good story and campaign mode. Bring on Heart of the Swarm!

23. Elder Scrolls III: Morrowind Game of the Year Edition (PC, also on X-box)

This game just shows why the Elder Scrolls series is considerred one of the best WRPG franchises in existence. A wonderful open world that's highly unique in it's art-style and architecture; cities made from the carcasses of giant crabs, nomadic tribes, mechanical ruins and a range of natural scenery. As soon as you get off the boat there is just so much to do, so many skills to learn, places to explore and guilds to join. One of the best open-world RPGs ever created. 

22. Age of Empires II + The Conquerors expansion (PC)

Sequel to the award winning Age of Empires and one of the greatest multiplayer RTS' ever created. The civs were well balanced, there was a whole range to choose from and each had their unique specialties (I both loved and cursed British longbowman!). Take your Civ from the Dark Ages, through to an era of castles and trebuchets, cavalry charges, infantry rushes, Korean war wagons and those blasted longbowman! A great RTS.

21. Gran Turismo 5 (PS3)

I believe this is the only racing/driving game on my list which shows you how highly I rate GT5 (although the new F1 games come mighty close to top 50). The driving physics as always are great, but it's the sheers amount of content and support from the devs that make this game so fantastic. The constant update of online events, patches and upgrades is astounding, especially for a game that already has such a huge amount of content. The new spec 2.0 is a great addition improving some of the inconsistencies and making the endurance races that bit more doable.

20. Fallout 3 (PC, also on 360 & PS3)

Fallout 1 & 2 were classic old-school RPGs. Fallout 3 is Oblivion with guns! When I found out Bethesda were doing the new game I was very excited and it didn't dissappoint. Large open sprawling world, the perks that made the original games great and an odd mix of old school Fallout atmosphere mixed with modern open-world Oblivion-esque gameplay. It just seemed to have a great mix of old and new WRPG elements. Nearly all of my gamer points are thanks to this game (A full 1500 thanks to the DLC!). The levelling system was great and exploring the each new area was actually a joy. The lessons learnt on Fallout 3 (and Oblivion for that matter) have also translated well into the new elder scrolls game Skyrim.

15. Super Mario World (SNES)

Mario has always been a major part of my gaming life, but for quite some time, SMW was my gaming life. I played nothing else until I found every single exit, got the maximum amount of lives and maxed out the score. It got to a point where I could probably play certain levels with my eyes closed. I've lost all that ability now, but I still love this game. And the funny thing is, despite all that I did with this game, it isn't my favourite Mario game, in fact it's not even close to being my favourite, as you'll see as this list reaches its conclusion.

19. Legend of Zelda: Link's Awakening (GB, also on GB Color & DS as DX)

I have a confession to make. This is the only Zelda game on my list! I'm still playing through OoT on VC, never completed A Link to the Past (which I really enjoyed) and Twilight Princess just missed out this year due to some top new releases. However, there's something to be said about the first time you play a Zelda game and this was my first. Maybe it was because I played it as a kid or maybe it was because it was the first Zelda game I'd played, but this fuelled my imgaination in ways most modern games don't even come close to realising. The charming 2D sprites coupled with the superb design of items, levels and game progression made this one of the greatest game's ever made. I pretty much played this and nothing else for a 1.5 years; it's just a joy to play.

15. Uncharted: Drake's Fortune (PS3)

Although I liked Uncharted 2 and 3 more than this, Drake's Fortune is still an amazing game and it was the start of one of my favourite franchises of all time.