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.

Layouts in each category are sorted roughly by my evaluation from best to worst.

Evolved layouts:

MTGAP's Layout
Xuming Zeng's RSTHD Layout
Michael Capewell's Evolved Layout
Carpalx Layout Optimizer
Peter Klausler's Evolved Layout
Optimized 1-Finger Layout
Chad Brewbaker's layout
Christopher P. Walker's layout
Keyboard Layout Optimizer – Travis Brown (incomplete)

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
Arensito
Amuseum's layout
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