Here's a lot of categories. Vote on your favourite Kojima Games in each.
Sorry about the drole introduction, but I wasn't very interested in writing one.

Best Plot-
Best Visuals-
Best Dubbing (Mention whether it's English or Japanese, too)-
Best Dialogue-
Best Game Design-
Best Character-
Best Boss Fight-
Best Puzzle-
Best Character Design-
Best Mechanical Design-
Best Overall Gameplay-
Best Remake/Special Edition pack-
Best Themetune-
Best Series-
Best Sequal-
Biggest Improvement-
Best "Kojima Moment"-
Best Kojima Game-
Here's my personal choices (with reasons), for each Category-
Best Plot- Snatcher- It seemed to be very well rounded, very well paced, and very well written. Overall, just great.
Best Visuals- MetalGear Solid 3: Snake Eater- A very obvious choice
Best Dubbing- MetalGear Solid 2: Sons of Liberty (English)- Seemed very professional, interesting and fit each character very well.
Best Dialogue- MetalGear Solid- Most quotable lines in any Kojima game, i've played.
Best Game Design- MetalGear Solid 2: Sons of Liberty- The game's saving grace. No complications with Camo choices and backpacks, yet you were able to take control of any situation.
Best Character- Grey Fox (MetalGear, MetalGear 2: Solid Snake, MetalGear Solid)- No brainer for me, a very passionate and cool character.
Best Boss Fight- Psycho Mantis- Does confuse the hell out of you. Exactly what Kojima wanted, and what no one else would've came up with
Best Puzzle- Blow up the rat! (MetalGear Solid)- Loved doing this, game me a worrying feel of power.

Best Character Design- Zone of the Enders: The Second Runner- Really fits the Anime theme.
Best Mechanical Design- Zone of the Enders: The Second Runner- Very interesting Frames. The huge battleships are fantastic, too.
Best Overall Gameplay- MetalGear Solid 3: Snake Eater- Very tense, and really makes you think about your choices. You're much more involved with boss battles, than before, too.
Best Remake/Special Edition pack- MetalGear Solid: Integral- Ninja missions, 1st person mode, Mystery mode, giant Genomes... fantastic.
Best Themetune- Zone of the Enders: The Second Runner (Beyond the Bounds)- Fast paced and exciting piece, that sums up the overall experience very well.
Best Series- MetalGear- Kojima's claim to fame, and full of brilliant titles. Constantly surprises Gamers.
Best Sequal- MetalGear 2: Solid Snake- Really did everything you wanted it to. Fighting against Big Boss and Grey Fox was a dream, after playing the first game.
Biggest Improvement- Zone of the Enders series- Wasn't very keen on the original, but the second game was a very good game with lots of different positive elements.
Best "Kojima Moment"- Runaway Turbocycle (Snatcher)- I loved this scene all the way through. I don't think i've laughed at a game so much, before.
Best Kojima Game- MetalGear 2: Solid Snake- Although I haven't voted for it in many other categories, it was the best all round game. Fantastic plot, puzzles, characters, and level design make this my favourite game of all time.