The ones used today is mainly from release X11R4. See below. That is: not only by name but also by definition.
Looking at Wikipedias entry on X11 color names it states that they
were defined by Bob Scheifler of MIT's Laboratory for Computer Science.
As he lead out the birth of X back in 1984 that is probably correct – but
the reference has no such claims.
Looking at one of the first releases, X.V10R3, another name pops out
when looking at the code, namely Tony Della Fera of MIT Laboratory for Computer Science, Digital Equipment Corporation (DEC) and Project Athena.
He did at least commit the rgb.c
file back in 86 ;)
static char *rcsid_rgb_c = "$Header: rgb.c,v 10.4 86/02/01 15:55:22 tony Rel $";
In the following release, X.V10R4, he is also credited in the man pages
for e.g. X and xload.
Anyhow is it rather safe bet to guess Bob Scheifler had at least a big part
in compiling the list given his role in the core start.
(A note from net.unix-wizards, X Window System Release 3 (Protocol Version 10) – Jim Gettys, Paul Asente, Brian Reid and Bob Scheifler on V vs W vs X on
origins, credit, etc.)
But; that does not mean he or they actually coined the names. It could also
origin form the Ultrix Window Manager as it got included in X. It at
least uses color naming like Aquamarine, MediumSeaGreen etc.
LINFO X Origins of X.
Colors by revision
X10R3 - X11R1 ; 1986 - 1987
The colors for release (Dates from here):
10R3 ca. 1986-06-07
10R4 ca. 1986-12-25
11R1 ca. 1987-09-18
are the same. 69 colors given by lowercase separated words and upper camel case.
E.g.:
255 240 245 lavender blush
255 240 245 LavenderBlush
X11R2, ca. 1988-03-24
In release 11R2 two new colors came along namely:
Brown 165 42 42
Gray 192 192 192
Grey 192 192 192
Yes, gray was by two names. From notes it also seems some people was happy
about this because they always forgot if it was grey or gray – ref.
xfd change suggestion by HP Labs:
X.V11R3/doc/bugs/database/closed/xfd/11
X11R3, ca. 1988-10-27
In release 11R3 there was a few changes SandyBrown
came along.
Until now white had been RGB 252 252 252
but now was changed to
255 255 255
.
101 shades of gray was also introduced. Going from
gray0 0 0 0
gray1 3 3 3
gray2 5 5 5
# ... to
gray100 255 255 255
# with a 3-2 interval.
That would mean, as both grey and gray was used – 202 new names.
Gray variants was used earlier as well but then mere in the form of:
menu = " CREATE WINDOW " {
Black: !"xterm -r -bw 3 &"
White: !"xterm -bw 3 &"
"Gray #1": !"xterm -bw 3 -bg LimeGreen -fg Black &"
"Gray #2": !"xterm -bw 3 -bg MediumSeaGreen -fg White &"
"Gray #3": !"xterm -bw 3 -bd White -bg DarkSlateGray -fg White &"
}
and various shades dynamically generated in C, and bitmaps such as gray3.bitmap:
#define gray3_width 16
#define gray3_height 16
static short gray3_bits[] = {
0x1111, 0x0000, 0x4444, 0x0000,
0x1111, 0x0000, 0x4444, 0x0000,
0x1111, 0x0000, 0x4444, 0x0000,
0x1111, 0x0000, 0x4444, 0x0000};
used to tile backgrounds etc.
X11R4, 1989-01-29
Then by release 11R4 came a major change
(X11R4/mit/rgb/others/README) by the hands of Paul Raveling at Information
Sciences Institute (ISI) of the University of Southern California and John C
Thomas at Tektronix, Inc. Oregon (at least).
They removed two and added 376 new colors but also redefined almost all colors.
These values are what stands today. A few has been added later.
Thomas, funny enough, among other things, did tuning by going trough 72 Crayola
crayons. Paul Raveling then did further tuning using his own HP monitor.
The README speaks for itself.

Image from http://blog.flauntme.com/2010/02/17/diy-crayon-lipstick/
Example of tuning:
-OLD- -NEW-
BlueViolet 159 95 159 BlueViolet 138 43 226
DarkGreen 47 79 47 DarkGreen 0 100 0
Firebrick 142 35 35 Firebrick 178 34 34
Added colors:
AliceBlue Gainsboro Linen PaleGoldenrod RosyBrown
AntiqueWhite GhostWhite MediumPurple PaleTurquoise RoyalBlue
Azure Honeydew MintCream PaleVioletRed SaddleBrown
Beige HotPink MistyRose PapayaWhip Seashell
Bisque Lavender Moccasin PeachPuff SlateGray
BlanchedAlmond LavenderBlush NavajoWhite Peru SlateGrey
burlywood LawnGreen OldLace PowderBlue Snow
DodgerBlue LemonChiffon OliveDrab Purple Tomato
WhiteSmoke
DarkGoldenrod DarkOrange DarkSeaGreen DeepPink
DarkKhaki DarkSalmon DarkViolet DeepSkyBlue
LightCoral LightGoldenrodYellow LightSeaGreen LightSlateGray
LightCyan LightPink LightSkyBlue LightSlateGrey
LightGoldenrod LightSalmon LightSlateBlue LightYellow
And also 312 shades like:
snow1 snow2 snow3 snow4
seashell1 seashell2 seashell3 seashell4
etc.
Removed:
MediumForestGreen 107 142 35
MediumGoldenrod 234 234 173
X11R5, 1994-05-18
Gray and grey was changed from 192 192 192
to 190 190 190
.
X11R6, 1995-03-02
New additions:
DarkBlue DarkCyan DarkMagneta DarkGray LightGreen DarkRed
X11R6 - DD.
None I'm aware of. Notice Wikipedia also list six W3C colors plus teal, olive, crimson, fuchsia, indigo and an alias for cyan as aqua.