This is a list of every alternative keyboard layout that I know of. If you find a keyboard layout that's not on here, please email me at mdickens93 AT gmail DOT com and I will add it to the list.

Evolved layouts:

Arno Klein's Engram Layout
Carpalx Layout Optimizer
Chad Brewbaker's layout
Christopher P. Walker's layout
Halmak Layout
Jeo Layout
Michael Capewell's Evolved Layout
MTGAP's Layout
Optimized 1-Finger Layout
Peter Klausler's Evolved Layout
Travis Brown's Keyboard Layout Optimizer
Xuming Zeng's RSTHD Layout

From colemak.com:

Colemak
nawfal's layout
BvoFrak EN Layout
SorenK's layout a.k.a. OSTNREAI
Seruxie's Layout
DreymaR's layout
Toss the spacebar

Based on QWERTY:

Norman Layout
Asset keyboard
Qwerak
Minimak

The rest:

Balance 12
Workman Layout
Nicholas Sterling's THE-1 Keyboard Layout (see also forum discussion)
Arensito
Amuseum's layout
Benkeyless
Maltron Layout
ADNW (German)
Neo (German)
BEPO (French)
DDvorak
Ulf's German Layout
nlite4 Keyboard Layout
Tim Tyler's Layout
Dvorak
Performance Optimization of Virtual Keyboards (research paper)
Slashdot page about alternative layouts
Plum
qwpr
XPeRT
Rick Harrison's layout
QWERTY

Layout analyzers:

Michael Dickens's Keyboard Layout Optimizer
Carpalx
Andong's Analyzer
Keyboard-C