1. Legend of Zelda: A Link to the Past ; A lengthy, fast-paced adventure with a fairly large, interesting world. There's a large number of pretty good dungeons. The overworld(s) have fun things to do and places to see, and the areas connect to one another in a cohesive, convenient manner rather than being spread apart from one another. This, and Super Metroid, are rare examples of adventures that seem to feature little to no filler.
2. Super Mario Galaxy 2 ; Favorite 3D (maybe overall) platformer. I think the Galaxy games are possibly the most creative and imaginative games of the series, while managing to remain fast-paced and lengthy. And it has excellent music, graphics and art design.
3. Super Mario World 2: Yoshi's Island ; This spinoff outshines the series that inspired it due to its unique shooting mechanic, charming artwork and creative level design. The secret levels are a challenge to both unlock and complete.
4. Super Metroid ; There's action from the beginning to the end, while providing plenty of secrets if one wants to take a break and explore. Part of me prefers the expanded environments, intense boss fights, and creative uses of the morphball found in the Prime series, but overall I think I prefer replaying this lean, fast-paced 2D action-adventure.
5. Metroid Prime ; A great expansion of Super Metroid's gameplay into three dimensions. The art, level design, enemies, puzzles, graphics and music are great, and scanning was a creative way of allowing the player to learn more about the world and its creatures. My one gripe is that fighting enemies sometimes feels like a chore, a feeling I have regarding almost all non-2D games. (Many Super Metroid enemies can be beaten in seconds or avoided. Battles against some Prime enemies take much longer and feel more repetitive.)
6. Metroid Prime 2: Echoes ; I enjoyed the emphasis on the morphball. It's used in ways I never would have expected. I like the large number of mid-boss and boss battles. The level design of the main areas is great (well, the first one is decent, but the others are really interesting and cool). Some parts feel like filler or have slightly too much backtracking.
7. Metroid Prime 3: Corruption ; I felt the others had slightly better bosses/level design. Aiming with the remote works well. The multiple planets make it the most disjointed of the Metroid games (in a way that reminds me of Skyward Sword's mini-overworlds), but they still feature plenty of the great level design, combat, music and art found in the other games.
8. Sin & Punishment: Star Successor ; It has varied level and enemy design, lots of bosses/midbosses, and it's fairly long for a rail shooter. At times, the screen looks like bullet hell, but the dodge mechanic makes it manageable. The two characters are different enough that I wanted to play through with both (also, because of the mode that is unlocked afterwards). I like that character movement (analog stick) and aiming/shooting (pointer/remote) are controlled independently unlike most rail shooters. That can technically be achieved with dual analog sticks, but it would definitely not feel as fluid or comfortable considering the hectic action of the game.
9. Legend of Zelda: Majora's Mask ; There's an unusually dark storyline, lots of interesting (and genuinely rewarding) sidequests and characters, and better pacing and less filler than most of the 3D Zeldas. I like that the world is densely packed into one central town and a small, surrounding field. (I like the idea of crossing a massive land, ocean or sky, but it can get boring.)
10. F-Zero GX ; Insane course designs and a great sensation of speed. The story mode was a good addition, though it was sometimes frustrating.
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Honorable mention:
Tetrisphere ; One of my most played puzzle games ever. It's weird, unique, lengthy, challenging and has a catchy electronic soundtrack.
Banjo-Kazooie ; A more challenging, less linear take on the Mario 64 formula. Felt like a platforming adventure.
Blast Corps ; Unique, challenging driving/flying destruction gameplay. Crazy unlockable bonus levels were a good incentive to aim for high scores.
Conker's Bad Fur Day ; Its gameplay and level design are humorously random, and it has great, fast pacing.
Perfect Dark ; The level/mission design, multiplayer options, bots and unique weapons make this one of my favorite shooters.
Donkey Kong (1994) ; Probably my favorite Game Boy game. They turned a fairly simple arcade game into a lengthy, addictive puzzle platformer.
Donkey Kong Country Returns ; Shake-to-roll annoyed me, but I really liked the level design.
Earthbound ; A nicely paced JRPG with interesting areas and scenarios. It has a refreshingly fun, lighthearted story compared to its often overly serious, badly written peers. (I still appreciate those overly serious peers, but they often make me cringe or make me laugh at inappropriate times.)
Legend of Zelda: Link's Awakening
Legend of Zelda: Oracle of Ages/Seasons
Legend of Zelda: Ocarina of Time
Legend of Zelda: Skyward Sword
Legend of Zelda: Twilight Princess
Metroid: Zero Mission
New Super Mario Bros. Wii
Super Mario Bros. 3
Super Mario Galaxy
Super Mario World
Star Fox 64 ; This (and Panzer Dragoon Orta) nearly ties Sin & Punishment 2 as my favorite rail shooter. Each has great levels, cool bosses, and decent replay value.
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Honorable mention, tier 2:
Art Style (series) ; Especially Cubello and Light Trax. I wish I had a DSi so I could try the DSiWare games.
Clubhouse Games ; This is a great, portable collection of card and board games, offering lots of options.
Picross DS
Planet Puzzle League
Tetris/DX/DS
Donkey Kong Country 2: Diddy's Kong Quest ; Favorite of the SNES games (didn't play the 3rd one)
Donkey Kong Jungle Beat ; Odd, but surprisingly fun control method (for the Gamecube version) combined with fast, score attack gameplay.
Legend of Zelda: Four Swords Adventures
Legend of Zelda: The Wind Waker
Mario Kart/64/Double Dash/Wii ; Great multiplayer games with family and friends. MK Wii is good, though Nintendo messed up Battle Mode. Each game has several amazing courses.
Metroid: Other M ; This game is really flawed, but it's not all bad. Tecmo/Nintendo managed to make a 3D game that's as fast-paced as its 2d predecessors. The idea of a Metroid with more emphasis on story is fine, but the one they chose to tell did not serve the franchise well. Parts of the game are nonsensical and hilarious (in all the wrong ways), especially the timing when Samus obtains the Varia Suit. Those slow, first-person parts were lame. Still, the area design was decent. The combat is simple, but fast and fun (more like the 2D games). The concept should really be streamlined and expanded upon in a sequel, with more imaginative level design and better writing.
Super Mario 64/Sunshine ; They offer a sense of exploration that the others sort of lack. Sunshine disappointed, but F.L.U.D.D. is awesome. I would like a Sunshine 2.
Super Smash Bros. Melee/Brawl ; I like the unique focus on level design and single-player content compared to other fighting games.
Wii Sports/Resort ; I had some good times bowling, frisbee golfing and shooting targets with my family.
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I think I would enjoy Advance Wars, Fire Emblem, Kirby Super Star, Metroid Fusion, Mother 3, Legend of Zelda: The Minish Cap and Picross 3D, but I haven't played them yet. Banjo-Tooie and Pikmin 2 are cool, but I never finished them.