Reprising and revising a list I originally posted on RPGGeek:
Swords and Wizardry - White Box is rules compatible (mostly) with classic D&D whitebox with some nods to Moldvay compatibility (namely, racial classes as options);
S&W Core is actually AD&D 1E mostly compatible. Both have an "BAB & ascending AC" option. Knockspell is the house organ for it.
Castles and Crusades (C&C) is a new engine with the same classes and levels supported as either white box (the Collector Box) or AD&D 1E PH (Hardcover), and roughly similar abilities.
Mechanically, very different from AD&D.
PDF and print editions for sale commercially.
Spellcraft and Swordplay is yet another different engine with AD&D comparability but not true compatibility. It uses 2d6 for checks for 11+, DM from stats and difficulties... and ascending AC (from 0), with magic bonuses not going to AC but penalizing opponents' attempts to hit.
Company Website: http://www.grey-elf.com/
Dark Dungeons is Alston's D&D Cyclopedia retrocloned, including Wrath of the Immortals' rules. A huge tome, it includes the War Machine, Immortals, general skills, weapon mastery... it lacks the Gaz and HWR classes, but otherwise, this is as close to a D&D Rules Cyclopedia as one can find new.
Old Blog: http://darkdungeonsblog.wordpress.com/
new site: http://www.gratisgames.webspace.virginmedia.com/
"Get It Now" Print and Free PDF: http://darkdungeonsblog.wordpress.com/get-it-now/
Darker Dungeons is thematically the same as Dark Dungeons, but uses the d20-System mode of 1d20+mods for TN or more. It uses the same core classes, plus a couple are added. Some other changes are also in there.
free PDF, links to PoD for print. Printer-friendly PDF available.
Darkest Dungeons is a warped and twisted set of rules based upon adding Cthulu Mythos to Darker Dungeons. Not yet available, but annouced.
Labyrinth Lord is essentially Moldvay style B/X D&D.
LL Advanced Edition Companion is essentially "AD&D as if Moldvay had redone it"
Company site: http://www.goblinoidgames.com/labyrinthlord.html
Osric is almost identical to AD&D1E PH and DMG mechanics, but reworded. Monks are missing due to the difficulty of rewording them...
Knights and Knaves Company and free PDF: http://www.knights-n-knaves.com/osric/
First Edition Society Print and free PDF: http://stores.lulu.com/firsteditionsociety
Forward To Adventure is a T&T influenced D20 stripdown with minimal compatibility (but monsters can be used pretty easily from D&D/AD&D/3E sources. Surprisingly well done, but its past the "No Longer D&D" stage. D&D modules, however, can easily be used with it.
Website, with obvious purchase links: http://www.flyingmice.com/FTA.html
Redbox Hack is unrelated mechanically, and is just old school in tone.
Blog and downloads: http://redboxhack.blogspot.com/
Searchers of the Unknown -"Another minimal way to play D&D" is D&D as if PC should have the same info as a monster stat block. Single page rules. Any D&D, AD&D, OSRIC, Labyrinth Lord, or Dark Dungeons module should be directly compatible.
free PDF: http://sites.google.com/site/wizardinabottle/searchers-of-the-unknown
Basic Fantasy is D20 D&D stripped down to Moldvay/Mentzer complexity.
free Open Office files (.odf) and PDF: http://www.basicfantasy.org/downloads.html
Mazes and Minotaurs is a mostly D&D white box inspired set of mechanics, but has streamlined, then folded, spindled, and mutilated them into something fun, simple, but not D&D anymore. It is of similar complexity to Moldvay.
Revised Mazes and Minotaurs is a slightly more detailed version, with some mechanical changes.
D&D modules can be run with minimal changes
Website and free PDF: http://storygame.free.fr/MAZES.htm
Lamentations of the Flame Princess is an AD&D-ish ruleset. I've not read it in detail, but it's pretty straight-forward.
Blog, Free partial PDF: http://lotfp.blogspot.com/ note that a content warning may block access.
Paid full PDF: http://www.indiepressrevolution.com/xcart/product.php?productid=17286
Hackmaster 4E is an AD&D 1E expanded and modified. Print only, out of print.
Hackmaster Basic is a new engine with the same tone as HM4E, but isn't mechanically compatible. Commercial release.
Publisher Website: http://www.kenzerco.com/
Myth and Magic is an AD&D 2E retroclone, but with 3E style Armor Class. Open playtest.
Dungeon Crawl Classics RPG is an OGL system by Goodman Games that cross-breeds Appendix N with a streamlined version of 3E. It's also described as pre-D&D swords & sorcery. It uses the d20 mechanism and save system of 3E, with classes from basic D&D, and combines other ideas such as random magic effects, Zocchi dice, a luck system, and 0-level character development.
Publisher Page: http://www.goodmangames.com/dccrpg.html
Adventurer Conqueror King System (also known as ACKS) is less of a retro clone and more of a Basic D&D tribute. ACKS takes the "D&D endgame" of strongholds and kingdoms, and uses it as the basis for the tier system that’s explicit in the game’s title. Adventurers are the typical dungeon-crawlers of most D&D systems. Conquerors earn lands and titles, shaping the wilderness into civilization. Kings are the rulers of kingdoms.
Publisher Page: http://www.autarch.co/