http://www.vgmuseum.com/mrp/metroidvania/games.htm - That's the starting point.
Side Note: They have Final Vision listed twice, and the 2 Battle Kid games are NES homebrew, not PC games. I also don't know why they list "The Underside" as being released... I don't really want to know why they don't include any Metroid or Castlevania fan-games that also fit this criteria, but whatever, I'll put them here, anyway.
I don't really care to email these peeps about any of this, but anyway, here's a list of 30+ more that aren't (currently) on that list. (Note: a few are hentai related. I ain't telling ya which ones; lel.)
I listed the games' general sources/homepages as well as the Kanji/whatever of the original titles for Japanese-released ones. (If you don't know, searching the Kanji/whatever-equivalent brings up the actual homepages and data on the game such as YouTube/Nicovideo videos or whatever if it's Japanese-only.) This is also a personal reference list for myself, because literally, I forgot quite a few of these until I actually dug through this. I know there's another Touhou fan-game that I've forgotten, except I know Remilia's the main character... if it was a "Metroidvania", that is.
PC:
Nue's Operation Bigburn (ぬえのビッグバーン大作戦) - http://utgsoftware.net/ (freeware, used to not be)
BlankBlood - http://ryonaproject.bake-neko.net/top.html (freeware)
Assault Crisis! (あさくら！) - http://somiso.pv.land.to/
Assault Crisis! 2 (あさくら！2) - http://somiso.pv.land.to/
Assault Crisis! 3 (あさくら！3) - http://somiso.pv.land.to/
Assault Crisis! Prologue (あさくら！P) - http://somiso.pv.land.to/
Vampire Castle - http://web.archive.org/web/20100924124718/http://rezet.rdy.jp/rezetia/
Bouhou Koumakyou ~Scarlet Family~ (某方紅魔郷 ～Scarlet Family～) - http://marokaka.net/
Bouhou Youyoumu (某方妖々夢) - http://marokaka.net/
Touhou Yuuen Sekai (東方遊宴世界) - http://spice.rash.jp/spice/index.html
Houchou Shoujo Gensoukyoku (包丁少女幻窓曲) - http://atelierizumi.org/ (freeware)
Houchou Shoujo Gensoukyoku: Memories of Replica (包丁少女幻窓曲: Memories of Replica) - http://atelierizumi.org/ (freeware)
GunGirl 2 - http://www.gungirl2.com/ (freeware)
Gun Princess (dead sources) (freeware)
Gun Princess 2 - http://www.64digits.com/games/index.php?cmd=view_game&id=5770 (freeware)
Hack9 - http://wahiko94.at-ninja.jp/ (freeware)
Hacker9 - http://wahiko94.at-ninja.jp/ (freeware)
Hack9 Solid - http://wahiko94.at-ninja.jp/ (freeware, unless a questionably named demo)
GHost9 - http://wahiko94.at-ninja.jp/
GHost92 - http://wahiko94.at-ninja.jp/
GHost93 - http://wahiko94.at-ninja.jp/
Viocide ～Vore Side Action RPG～ - http://xi.rdy.jp/xisite/top.htm
HOLDOVER - http://www.foxeye.squares.net/game.htm (freeware)
Sacrifice Girl -The Curse of Demon Snake- (生贄娘 -鬼蛇の呪い-) - http://www.foxeye.squares.net/game.htm (freeware)
Yakouga 3 (夜光蛾3) - http://artesneit.halfmoon.jp/fortuna/index2.htm
FairyAttackers - http://www.geocities.jp/dij4121/alpha/ (freeware)
Grounstream - http://www.geocities.jp/dij4121/alpha/ (freeware)
GuardianTwins - http://www.geocities.jp/dij4121/alpha/ (freeware)
Tria: The Island in the Sky (空浮かぶ島のティリア) - http://www.geocities.jp/dij4121/alpha/ (freeware)
Wonderful Pink (ワンダホーピンク) - http://tifa.tank.jp/
LAB-Still Alive- - http://nekonomemegame.blog.fc2.com/
The Nameless - http://exile.ovine.net/ (freeware)
The Labyrinth of Holy Magic (聖魔の迷宮) - http://porita9.blog.fc2.com/
Nightmare Sphere - http://page.freett.com/mickmanx/NS/ (freeware)
The Paradise Fortress of RePure Aria (楽園魔城リピュアリア) - http://repureria.x.fc2.com/gametop.html
Metroid Redemption - (dead sources, including author's archived homepage) (freeware)
Metroid: The Egg Hunt - http://metroidr.brpxqzme.net (freeware) (inclusive of any others that might be on that site)
ワビの冒険3 糸星人の復讐+α (I'm not gonna try to translate it) - http://www.vector.co.jp/soft/win95/game/se478030.html (freeware)
女帝囚人H (no translate) - http://isa68.x.fc2.com/top.htm
UnEpic (On Steam somewhere; not looking)
Valdis Story: Abyssal City (On Steam somewhere)
Destroy Girl Kanon-chan (デストロイ少女☆カノンちゃん) - http://ekuran1111.blog.fc2.com/
Witch Girl Sayurin's Magical Quest (魔女っ子さゆりんのまじかるクエスト) - http://web.archive.org/web/20130227203412/http://chinchilla.xsrv.jp/game/sayuri/index.html
Witch Girl Sayurin's Magical Quest 2 (魔女っ子さゆりんのまじかるクエスト2) - http://web.archive.org/web/20130227204928/http://chinchilla.xsrv.jp/game/sayuri2/index.htm
モン姦リョナアクション - http://aclass.rojo.jp/a/mkract.html
PC "Overworld-Divided": (going by that site, I guess)
Touhou Splinter Cell Code:R (東方スプリンターセルCODE:R) - http://www.blue-mica.com/
Super Panda Adventures - http://www.paulinthenet.de
(I don't know if you could count Pirates of the Caribbean: Dead Man's Chest for GBA in this "Overworld-Divided" category; just mentioning it.)
PC 3D:
Another Bound (not on author's site anymore, I think I got it from Caiman.us, might be dead) (freeware)
Another Bound Neo - http://hp.vector.co.jp/authors/VA029904/ (freeware)
(I don't even want to know how "3D Metroidvania" makes any amount of sense. Anyway, this is a Metroid Prime-esque clone and its slightly updated remake... I'd love to know how to unlock the last set of images, dammit)
PC: (Currently) Unreleased
Mega Man X: Corrupted - https://www.facebook.com/JKBGames (freeware)
Metroid: Father Hunt - http://metroidcomical.blogspot.com/ (freeware)
Project AM2R (Another Metroid 2 Remake) - http://metroid2remake.blogspot.com/ (freeware)
Metroid Prime 2D - http://z3.invisionfree.com/MP2D/index.php? (freeware, still not dead yet, lel)
GHost94 - http://wahiko94.at-ninja.jp/
Nightmare Sphere 0 - http://page.freett.com/mickmanx/NS/
P.S.: Houchou Shoujo Gensoukyoku and the sequel are Yume Nikki fan-games... both of which I find better than the source material; lel.
FairyAttackers and the others by Alpha Secret Base are styled after Monster World IV for the Genesis, including sound effects.
Update: So, here's this list I found: https://docs.google.com/spreadsheet/ccc?key=0Audjc8k7dnB0dERfd0Rub04yeGhDSkJvb19jQmVib3c#gid=0
Oh yeah, that whole "3D Metroidvania" stupidity still applies; lel. I listed a bit of these over there.
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