It consists of ensuring that flags that either only work on Windows or only work on Linux/OS X appear just in the flag files for the platforms that support them (as is already done with -nograb), as well as adding a link to the new wiki stub entry on soft particles. If there are other flags like these two that should have #ifdef SCP_UNIX / #ifndef SCP_UNIX ... #endif around them, please let me know and I'll add them to the patch.
Other than that, let me know what you think. Thanks.
Index: code/cmdline/cmdline.cpp
===================================================================
--- code/cmdline/cmdline.cpp	(revision 7508)
+++ code/cmdline/cmdline.cpp	(working copy)
@@ -123,7 +123,7 @@
 	{ "-normal",			"Enable normal maps",						true,	EASY_MEM_ALL_ON,	EASY_DEFAULT_MEM,	"Graphics",		"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-normal" },
 	{ "-3dshockwave",		"Enable 3D shockwaves",					true,	EASY_MEM_ALL_ON,	EASY_DEFAULT_MEM,	"Graphics",		"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-3dshockwave" },
 	{ "-post_process",		"Enable post processing",					true,	0,					EASY_DEFAULT,		"Graphics",	"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-post_process" },
-	{ "-soft_particles",	"Enable soft particles",					true,	0,					EASY_DEFAULT,		"Graphics",	"" },
+	{ "-soft_particles",	"Enable soft particles",					true,	0,					EASY_DEFAULT,		"Graphics",	"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-soft_particles" },
 	{ "-fxaa",				"Enable FXAA anti-aliasing",					true,	0,					EASY_DEFAULT,		"Graphics",	"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-fxaa" },
 
 	{ "-img2dds",			"Compress non-compressed images",			true,	0,					EASY_DEFAULT,		"Game Speed",	"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-img2dds", },
@@ -167,7 +167,9 @@
 	{ "-ati_swap",			"Fix colour issues on some ATI cards",		true,	0,					EASY_DEFAULT,		"Troubleshoot", "http://scp.indiegames.us/mantis/view.php?id=1669", },
 	{ "-no_3d_sound",		"Use only 2D/stereo for sound effects",	true,	0,					EASY_DEFAULT,		"Troubleshoot", "http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-no_3d_sound", },
 	{ "-disable_glsl_model","Don't use shaders for model rendering", true, 0,		EASY_DEFAULT,		"Troubleshoot", "http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-disable_glsl_model", },
+#ifndef SCP_UNIX
 	{ "-disable_di_mouse",  "Don't use DirectInput for mouse control", true, 0,		EASY_DEFAULT,		"Troubleshoot", "", },
+#endif
 	{ "-use_gldrawelements","Don't use glDrawRangeElements",			true, 0,	EASY_DEFAULT,		"Troubleshoot", "", },
 
 	{ "-ingame_join",		"Allow in-game joining",					true,	0,					EASY_DEFAULT,		"Experimental",	"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-ingame_join", },
@@ -176,8 +178,9 @@
 	{ "-fps",				"Show frames per second on HUD",			false,	0,					EASY_DEFAULT,		"Dev Tool",		"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-fps", },
 	{ "-pos",				"Show position of camera",					false,	0,					EASY_DEFAULT,		"Dev Tool",		"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-pos", },
 	{ "-window",			"Run in window",							true,	0,					EASY_DEFAULT,		"Dev Tool",		"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-window", },
+#ifndef SCP_UNIX
 	{ "-fullscreen_window", "Run in fullscreen window",				false,	0,					EASY_DEFAULT,		"Dev Tool",		"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-fullscreen_window", },
-
+#endif
 	{ "-stats",				"Show statistics",							true,	0,					EASY_DEFAULT,		"Dev Tool",		"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-stats", },
 	{ "-coords",			"Show coordinates",						false,	0,					EASY_DEFAULT,		"Dev Tool",		"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-coords", },
 	{ "-show_mem_usage",	"Show memory usage",						true,	0,					EASY_DEFAULT,		"Dev Tool",		"http://www.hard-light.net/wiki/index.php/Command-Line_Reference#-show_mem_usage", },