This year has two major highlights for me. Major? No, gigantic highlights, so the final choice will nevertheless be easy. These two are high in my personal top 10, and one is one of my most played games ever. 2003 just because of those would score exceptionally high as a year already, but it still doesn't end there.
Off the lists in OP, besides the two 'big ones', my other favourites are Call of Duty and Anno 1503. The original Call of Duty is great. It is a very accessible first person shooter without too many complications. And I don't like complicated things, I just want to go in and have fun. It has a great campaign mode, but it even had me play a lot of multiplayer matches and there aren't a lot of games where the multiplayer interests me much if at all. The sequel to this is also great, but I lost interest in the series when they moved away from the World War II setting. Then Anno 1503, which built upon predecessor Anno 1602, one of my all-time favourite games. 1503 wouldn't reach it's height, but it still included many elements I wished had been included in later entries in the series; like the small church building becoming fancier when there are higher class houses within its range, or parks and beautification being an actual necessity. Next to those I also played Mario Kart Double Dash quite a bit, but it wouldn't grow to be one of my favourites, and like Mario Sunshine and The Wind Waker, I'd see it as inferior to it's N64 predecessor. The two character mechanic is essentially useless and I never liked as many of the courses. Still, fun times were had, particularly with my cousin.
2003 was also the year of the rts's Age of Mythology, Command and Conquer Generals and Rise of Nations and action games Enter the Matrix, LotR Return of the King and Star Wars Jedi Knight Jedi Academy. Other things this year include the GBA port of Super Mario Bros. 3 and Warcraft III's The Frozen Throne expansion and two games we already covered in 2002; the European release of The Wind Waker along with the so-called 'Collector's Edition' which included ports of Zelda 1 and 2, Ocarina of Time and Majora's Mask to GameCube and the great console version of SoulCalibur 2. All these would get plenty of playtime from me, the PC games in particular. Star Wars Jedi Knight Jedi Academy and Age of Mythology deserve an extra mention here, especially the latter. While Jedi Academy was great, because more Jedi Knight is great, I would always prefer Jedi Outcast. Age of Mythology is already great as an rts by the maker of Age of Empires, but the mythological aspect with magical heroes and gods really interested me beyond that, and it added depth and made the game much more replayable for me. It remains one of my all-time favourites, but it would however be the last new rts I'd really be into, because my interest would shift to a different style of strategy game soon.
All these games however, are dwarfed by juggernauts SimCity 4 and Star Wars Knights of the Old Republic and these would pretty much doom my interest in console gaming altogether for the next half decade.
SimCity 4, to start, was a game I anticipated greatly and it was the first game I ever pre-ordered. I had already played previous SimCities to death and was ready for more, more and better. It was all I wanted, and basically the perfect city builder. What I especially liked was the way your cities were connected to each other via a 'region'. Basically the screen to select your savegames on as you saw your cities as if from a plane, but I would go out of my way to make the region one coherent country with a 'capital' (imaginary, it wasn't like you could really designate something as such), rural areas, a port city and whatever else I could come up with. I spend hours, days, months, years, no, decades on them. One day I found out that you could manipulate the shape of a region (which initially is just rectangular) and the position and amount of the different city sizes in a region by fiddling with a certain image file. Of course, at that point all bets were off. Luckily I still have most save files and regions, later ones including loads of custom assets, so I can revisit all my work.
Then lastly, at first I was hesitant about Star Wars Knights of the Old Republic when I saw it. It looked slow paced, while I was accustomed to flashy action with things like Jedi Outcast, and its story took place thousands of years before the movie-era so there were no familiar characters or even locations for the most part. My mother however tried it out, by illegally downloading it at first of course, and watching her play, I was quickly sold. This game would grow to become my second favourite video game of all-time. A game with the best story, dialogue and twists, amazing areas and locations, memorable characters and the greatest villain, great music and backdrops, loads of content both main and side and actually plenty of action. It is the best rpg I ever played, the best Star Wars game that probably will ever exist, and almost the best video game I ever played. When I completed it for the first time, I was bummed it was over, and immediately started another playthrough. Really, you should play it at least four times through anyway, because it matters whether your character is male or female, and light or dark. So I did just that; a light male, a dark male, a light female and a dark female. And then, I played through some more without a plan just to see where I'd end up with.
If it wasn't clear, my vote easily goes to Star Wars Knights of the Old Republic, even SimCity 4 can't beat that.
Also, include Knights of the Old Republic in your Top 50 list for mZuzek's thread. It is criminal it wasn't in the top 100 last year.