Straight from the mothership, Big N has high-resolution manuals for your perusal. It's not ip infringement if Nintendo is hosting this themselves, right?
Hint: Hit Ctrl + F on your keyboard to find what you're looking for faster.
Game Boy Advance
Advance Wars
http://media.nintendo.com/nintendo/bin/Ir5KqLnGnZuQQnReTNynS6IIQnf4KIil/NtneaDypx_Yj1AFX6FGMvB-dI1G7k5ZD.pdf
Castlevania: Aria of Sorrow
http://media.nintendo.com/nintendo/bin/T46Su7skRGQpepz9G-0MlRVh5YBLmMm1/zWXy_OCG1tTEnLDYgClhTk0Fb0xNERDh.pdf
Castlevania: Circle of the Moon
http://media.nintendo.com/nintendo/bin/xIn3HAmTYu53Xkc5Wk5V9rEmewNHBW-o/tCxGXwVCb2PH49Pos6m_DO7DDM6zTldt.pdf
Castlevania: Harmony of Dissonance
http://media.nintendo.com/nintendo/bin/I7M-P2JpPp9bc7owQ60yO6VdGBoXIAVa/4O3q3AjkTvmo0ya9Jpl6WLU1YxPvO7Xn.pdf
DK: King of Swing
http://media.nintendo.com/nintendo/bin/iTWgYiJG7AsuXOWvVPBioZ8XcHmIAQGa/y8FarK92oe0SB31kUAkBlJA1yK5E2Z2r.pdf
Fire Emblem
http://media.nintendo.com/nintendo/bin/WWGe4B9TS7VbRC0V6x-OJAVBDuEiVbOX/mPPXIGoDaQbobJ89fOsAF5vVitgDImrl.pdf
Fire Emblem: The Sacred Stones
http://media.nintendo.com/nintendo/bin/hEdz6QCdBMbBoGW9NNCPXH25oCbd4rt3/mSxVebfnU-p96pOI-Il7-f8tOIkQ4bQD.pdf
F-Zero: GP Legend
http://media.nintendo.com/nintendo/bin/ekaoadQwOqWE1yv3Lnczv5c_4iLd_Ivs/JmRz25ZxGT5dJRYSH1iMn7itnMpnSTn0.pdf
F-Zero: Maximum Velocity
http://media.nintendo.com/nintendo/bin/vs1EfwYo1398MOSdbsqS4jAMjEX4z_BF/ixBO0uwcHtYSH0aP8wt3ItFEqCAHVVNe.pdf
Golden Sun
http://media.nintendo.com/nintendo/bin/E7IUHJ9xjphZC_Dt9xq58Oj1sMKwsBAD/Yi2A9Y4z3rWZzpncCScXIuEWhzJqyPCp.pdf
Harvest Moon: Friends of Mineral Town
http://media.nintendo.com/nintendo/bin/BueFUqxUtEdiA9_SQWoKHtJPVGvhDGdK/pBuwlrJxWOqJT6-fxp9IjB0yJKRu3juP.pdf
Kirby & The Amazing Mirror
http://media.nintendo.com/nintendo/bin/YM8ciZJMd8qIg5dj8N4NlpgR1ZGgvzIc/aOYDt4BLVzeDAr5KnZpbDNpJsBXKmYUJ.pdf
Kirby: Nightmare in Dreamland
http://media.nintendo.com/nintendo/bin/jEOyZByzjiD5FKo588aCtAHcNpSBGlgB/DDJ8ht0qjJymItl2N0i10vBt57-Sdp5W.pdf
Klonoa: Empire of Dreams
http://media.nintendo.com/nintendo/bin/apA-N7kyTkA0-5Gvpa_39XRicL94nfz-/bLNUau5sU1Hh6JxeUqqQ7iREr2zuPpxK.pdf
Mario & Luigi: Superstar Saga
http://media.nintendo.com/nintendo/bin/avtLeUZzVIj4lxF8ySlthtu1umJLpYXf/zFmjddXMdMQOm7sJgrmVdIY55f45NOyK.pdf
Mario Golf: Advance Tour
http://media.nintendo.com/nintendo/bin/5kHhPUhCM7EI0i2djwX1NW6E6P2C9T0V/0zLy9BOXsHFjW-5TlSXcOZSkY6hS8spN.pdf
Mario Kart: Super Circuit
http://media.nintendo.com/nintendo/bin/n09QtHXIg5F5gf5oPjbjR6TBWdmXdORQ/_au7TexLHWAGAT4kTnbVoc5Ltt1F0Oyt.pdf
Mario Tennis: Power Tour
http://media.nintendo.com/nintendo/bin/757oTaS-7lbU4o6B2CA1MWr2EH9KkxMl/-zCv1VL6Y1UgeYzj5U6Bn8O2X0dC01CB.pdf
Megaman & Bass
http://media.nintendo.com/nintendo/bin/gQnxjfuC0Mng5zexkE4sTXaKGxb9mxjQ/t3BZqAExlFqMAHBtL5cfHEhn4TbF7t9A.pdf
Megaman Battle Chip Challenge
http://media.nintendo.com/nintendo/bin/QvdBITDpVEV-yNK98w9hitiVX3T_mQy6/nARKPF8VMsuLqlPEB_np2ayWrC0RkrWE.pdf
Megaman Battle Network 2
http://media.nintendo.com/nintendo/bin/na4KiXpnViJAwi1UysMELy-_iAisRNgh/UNEFnEXMZWqblA9wt37vdUF0UewJA_wr.pdf
Megaman Battle Network 3: White Version
http://media.nintendo.com/nintendo/bin/_MWyZCmIOA4IX73VCQOIabKPLSNOVitL/8S8gW3MBPGa-k80yHeK6eC8_bQgy3pLp.pdf
Megaman Battle Network 3: Blue Version
http://media.nintendo.com/nintendo/bin/iEhWJxtoS9xW9LV75wAjwwlkRntytzgw/iV47eHMI14mclWSIZ7gQROX7qz00sOZw.pdf
Megaman Battle Network 4: Red Sun
http://media.nintendo.com/nintendo/bin/l0NtJNE0ff7O-dNCnviyHQO6vbrYRP3h/cGir3OHMp6kaoJE6eXXJg3gL3po9EFho.pdf
Megaman Battle Network 4: Blue Moon
http://media.nintendo.com/nintendo/bin/KMWPHycrCzzLVMO5g4_UcS8CX8dnd5Ya/fOYMlz4x8OuOwmiLRuZxeriVyguDNYhg.pdf
Megaman Zero
http://media.nintendo.com/nintendo/bin/GVIjk7OAz_iqmtoco_oMfj5pIGcZR4re/kDIO7j_w9d3aAqwjbYfUfww-p72EZdHU.pdf
Megaman Zero 2
http://media.nintendo.com/nintendo/bin/p2PuNh9gqK1HcvIRapzRAJxufa8EOF70/pXmXV-CzuXwJsdojPg3LUktGbxrUe-MF.pdf
Megaman Zero 3
http://media.nintendo.com/nintendo/bin/a6ja5qqh0cZx8U6QEt6hKVky_dOYrSW3/iv1m6sF_CZZxt5-taUW_f6kDSUTgI0i6.pdf
Metroid Fusion
http://media.nintendo.com/nintendo/bin/EDlJl5ZTS9fdTwCQsCEQeKU2tyCKFsko/Qvp-5rypVoSEwuCqeFC9_g5MRXxeQK9a.pdf
Mr. Driller 2
http://media.nintendo.com/nintendo/bin/mq2La_d-yO0WGhTx130FVzsb37UmxrZk/TSEKq_WARlJ3zSqOQsoc7TukZiDrJ5E4.pdf
Namco Museum
http://media.nintendo.com/nintendo/bin/dJ7X0dGlE5vWs_JRvdCr8vPnV1MxeOrX/xuWfLw_VqCRVP--rJMOZAvj6gEq0o0Wv.pdf
PAC-MAN Collection
http://media.nintendo.com/nintendo/bin/auzgZOxZmriaQsv8zH447BrP981tf-Sm/wKh1PFD8DfASbzRBQboPRyYhpKi1Kxah.pdf
Pokemon Pinball: Ruby & Sapphire
http://media.nintendo.com/nintendo/bin/N9PHK84emyxDsGLX2FI465TqyUxrGwmT/3myqOIYV8adxIUEXsFIOuX5-Ys7MmCw7.pdf
Super Mario Advance
http://media.nintendo.com/nintendo/bin/pmfZgCN-Fp3-h7y9ttQEkaL9n3v8rMsg/wKzgcsrYCgxTVEqxihMWOxqVJzdozYM5.pdf
Super Mario Advance 2
http://media.nintendo.com/nintendo/bin/FE-Uh5E9tHuRbPiphRVeIdzr-_Pk33IG/D0RPxCfzu0nPYJn3zXvG-mceVB9MQJYv.pdf
Super Mario Advance 3
http://media.nintendo.com/nintendo/bin/cFg-_A_19Z5kIFpueVULlXeJvnLwkpmJ/0G8284k1l6kRXCsz4u1NOMlsfkJtNrWp.pdf
Wario Land 4
http://media.nintendo.com/nintendo/bin/H0f5-_aDjrrZy3lIpn-r-tG3vcCYOFUt/uUUuZ5pCq2aqQKKBDjbr9KwLQhW4TAxv.pdf
WarioWare, Inc. Mega Microgame$
http://media.nintendo.com/nintendo/bin/Z32GyS8cFh_Xmvipn9Sl8uziO57dUXjn/WrciXy4lbf-v6tuqO6v3Xr-BoYollElV.pdf
Nintendo Entertainment System
Balloon Fight
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAARE.pdf
Bubble Bobble
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABKE.pdf
Castlevania
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABQE.pdf
Castlevania II: Simon’s Quest
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABXE.pdf
Donkey Kong
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAEE.pdf
Donkey Kong Jr.
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAFE.pdf
DOUBLE DRAGON II: THE REVENGE
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NACHE.pdf
Dr. Mario
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAXE.pdf
Excitebike
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAHE.pdf
FINAL FANTASY
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABJE.pdf
Galaga
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABNE.pdf
GHOSTS 'N GOBLINS
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABCE.pdf
GRADIUS
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABRE.pdf
Ice Climber
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAUE.pdf
Kid Icarus
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAVE.pdf
Kirby’s Adventure
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAPE.pdf
Mario Bros.
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAWE.pdf
MEGA MAN 2
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABBE.pdf
Metroid
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAQE.pdf
NINJA GAIDEN
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NACBE.pdf
PAC-MAN
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABME.pdf
Punch-Out!!
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAATE.pdf
StarTropics
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAZE.pdf
SUPER C
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NABVE.pdf
Super Mario Bros.
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAAAE.pdf
Super Mario Bros. 2
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAADE.pdf
Super Mario Bros. 3
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAACE.pdf
Techmo Bowl
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NACDE.pdf
The Legend of Zelda
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAANE.pdf
Zelda II: The Adventure of Link
https://www.nintendo.co.jp/clv/manuals/en/pdf/CLV-P-NAASE.pdf
NINTENDO 64
1080° Snowboarding
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_1080Snowboarding_EN.pdf
Bomberman 64
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_Bomberman64_EN.pdf
Donkey Kong 64
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_DonkeyKong64_EN.pdf
Excitebike 64
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_Excitebike64_EN.pdf
F-Zero X
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_FZeroX_EN.pdf
Kirby 64: The Crystal Shards
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_Kirby64TheCrystalShards_EN.pdf
Mario Golf
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_MarioGolf_EN.pdf
Mario Kart 64
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_MarioKart64_EN.pdf
Mario Party 2
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_MarioParty2_EN.pdf
Mario Tennis
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_MarioTennis_EN.pdf
Paper Mario
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_PaperMario_EN.pdf
Pokémon Snap
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_PokemonSnap_EN.pdf
Sin and Punishment
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_SinAndPunishment_EN.pdf
Star Fox 64
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_LylatWars_EN.pdf
Super Mario 64
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_SuperMario64_EN.pdf
The Legend of Zelda: Majora's Mask
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_TheLegendOfZeldaMajorasMask_EN.pdf
The Legend of Zelda: Ocarina of Time
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_TheLegendOfZeldaOcarinaOfTime_EN.pdf
Wave Race 64
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_WaveRace64_EN.pdf
Yoshi's Story
http://cdn02.nintendo-europe.com/media/downloads/games_8/emanuals/nintendo_8/Manual_Nintendo64_YoshisStory_EN.pdf
UPDATE: I started this thread just to share a collection of Gameboy Manuals. My fellow Racketeers pointed out to me that Nintendo is hosting more manuals than just the Gameboy ones I initially shared here. So, I'm re-organizing this first post to incorporate some of the data that has since emerged. Many thanks to everyone who contributed so far.
