Please note, these keywords are case sensitive for now.

--Interface--

Sets the width and height of the application in pixels.
[WIDTH:800]
[HEIGHT:600]

To launch the application in windowed mode, set this to YES. 
Setting it to NO makes the program attempt to launch fullscreen mode,
using WIDTH and HEIGHT for resolution. Try and use resolutions compatible
with your drivers, or the program will still load in window mode.
[WINDOWED:YES]

These two options set how large the cube loaded from Dwarf Fortress is.
Each entry expects the number of tiles to load.
[SEGMENTSIZE_XY:70]
[SEGMENTSIZE_Z:3]

Change this to off to skip the intro.
[INTRO:OFF]

Changes the interface font size.
[FONTSIZE:10]

Changes the fontfile to use.
[FONT:DejaVuSans.ttf]

Lifts the segment up to the top off the screen, equivalent to a given
number of z levels.
Use this with a large segment size to get walls covering the entire screen.
[LIFTSEGMENT:0]

Follow DF window is on when Stonesense launches. (Toggle with 'f')
[FOLLOW_DF_SCREEN:YES]

Follow the center of the DF window, rather than scale to the edges.
[TRACK_CENTER:YES]

Sets an initial x/y/z offset for follow mode
[FOLLOW_OFFSET_X:-15]
[FOLLOW_OFFSET_Y:0]
[FOLLOW_OFFSET_Z:0]

Shows building graphics for zones. (Toggle with 'i')
[SHOW_ZONES:NO]

Shows building graphics for stockpiles. (Toggle with 'u')
[SHOW_STOCKPILES:NO]

Sets weather screenshots should have transparent backgrounds
[TRANSPARENT_SCREENSHOTS:NO]

Fog color, and alpha at the bottom z-level.
Setting the alpha to 0, or SHOW_FOG to NO disables fog, for a slight performance increase.
Color and alpha ranges are 0 (min) to 255 (max)
[SHOW_FOG:YES]
[FOG_RED:128]
[FOG_GREEN:158]
[FOG_BLUE:177]
[FOG_ALPHA:30]

Background color. setting this the same as the fog color produces a nice effect.
[BACK_RED:128]
[BACK_GREEN:158]
[BACK_BLUE:177]

This value, in milliseconds, is how long Stonesense waits between
reloading the map. If zero, the autoreload will be disabled until
set with Numpad+. Note that this will only work if a DF map is
ready when Stonesense loads.
[AUTO_RELOAD_TIME:50]

Amount to change the auto reload time with each press of Numpad+/-
[AUTO_RELOAD_STEP:50]

Amount of time, in milliseconds, before the animation swaps to the next frame.
Now independant of map refresh.
[ANIMATION_RATE:196]

--Adventure Mode Settings--

Sets weather Stonesense should use a day/night effect.
[NIGHT:NO]

Sets weather Stonesense should shade in the fog-of-war partially hidden tiles.
[FOG_OF_WAR:YES]

--Debug Mode--

Sets Stonesense in debug mode. Adds additional information to displays.
[DEBUGMODE:YES]

Set's the debug cursor to follow the cursor from DF when it is there.
[FOLLOW_DF_CURSOR:YES]

Shows creatures names floating above their sprites. (Toggle with 'n')
[SHOW_CREATURE_NAMES:YES]

Options to control how names are displayed (if SHOW_CREATURE_NAMES is set)
[NAMES_USE_NICKNAME:YES]
[NAMES_USE_SPECIES:YES]

Enables or disables the entire on-screen-display overlay (Toggle with F2)
[SHOW_OSD:YES]

Shows all creatures, for debugging. Living, dead, kidnapped, caged, EVERY single one.
[ALLCREATURES:NO]

Adds more logging information to what is written to stonesense.log. May be useful
if trying having issues with sprite configuration tweaking.
[VERBOSE_LOGGING:NO]

--Troubleshooting--

This is the number of draw operations that will be held at a time.  Holding draw operations allows 
for those draws to be carried out efficiently if they have the same source.  May be tweaked for
performance gains.  
[BITMAP_HOLDS:4096]

Stonesense will try to merge all loaded sprites into a single texture, for performance reasons.
if your videocard has low memory, you may want to disable this.
[CACHE_IMAGES:NO]

This set's the preferred size of the internal image cache. If your videocard does not support it, 
a smaller size is used.
[IMAGE_CACHE_SIZE:4096]

If this is set to YES, Stonesense will save a copy of the image cache each time something is added to it.
Dot NOT turn this on unless something is going very wonky. this will slow loading times considerably, 
and possibly quickly fill up yout hard-drive.
[LOG_IMAGECACHE:NO]

Set the preferred renderer. Valid values are SOFTWARE, OPENGL, DIRECTX, and ANY. SOFTWARE has the highest 
compatibility, but is very slow.
[RENDERER:OPENGL]

--Colors--

Stonesense can use the colors from DF for various purposes. these are set here the same way as in DF

[BLACK_R:0]
[BLACK_G:0]
[BLACK_B:0]
[BLUE_R:13]
[BLUE_G:103]
[BLUE_B:196]
[GREEN_R:68]
[GREEN_G:158]
[GREEN_B:53]
[CYAN_R:86]
[CYAN_G:163]
[CYAN_B:205]
[RED_R:151]
[RED_G:26]
[RED_B:26]
[MAGENTA_R:255]
[MAGENTA_G:110]
[MAGENTA_B:187]
[BROWN_R:120]
[BROWN_G:94]
[BROWN_B:47]
[LGRAY_R:185]
[LGRAY_G:192]
[LGRAY_B:162]
[DGRAY_R:88]
[DGRAY_G:83]
[DGRAY_B:86]
[LBLUE_R:145]
[LBLUE_G:202]
[LBLUE_B:255]
[LGREEN_R:131]
[LGREEN_G:212]
[LGREEN_B:82]
[LCYAN_R:176]
[LCYAN_G:223]
[LCYAN_B:215]
[LRED_R:255]
[LRED_G:34]
[LRED_B:34]
[LMAGENTA_R:255]
[LMAGENTA_G:167]
[LMAGENTA_B:246]
[YELLOW_R:255]
[YELLOW_G:218]
[YELLOW_B:90]
[WHITE_R:255]
[WHITE_G:255]
[WHITE_B:255]


Source: http://df.magmawiki.com/index.php/Color_scheme#ixzz0nnC90qXc
