Hi,
I've decided to start modding DesMuMe. I release here my first mod. It does not improve game compatibility but it has more features. It is only for Win32 users.
-First, I've added joystick support through SDL. That was easy.
-Next, I've added support for SDL sound core under Win32. That was easy too, the SDL sound core was here already.
-Added Vertical resize option. It was harder, I spent some time to add this. When activated, the window can be resized only vertically, the screens keep their size and the gap between the screens will be filled with your favourite colour (approximative). This allows users to set a gap depending on the game to get better gameplay.
Enjoy !!! Mod 2 is out with some fixes !!! 
-New GUI, added a toolbar and a statusbar to make it more user-friendly.
-Fixed LDR and LDM** opcodes, now opcodes are 100% correct (Thanks to Shash)
-Fixed Frame limitation when frameskip is 0
-Fixed some opcodes which prevented the emu to continue execution
-Fixed a stupid bug in the 3D core, this fixes Rayman Raving Rabbids 2, this should fix all other games that send unpacked commands to GXFIFO with reversed byte order (ie 0x1b000000)
-Added Wireframe 3D
-Fixed New Super Mario Bros minigames, thanks to Shash
-Added Video Capture option (sound & compress don't work yet)
-Started implementation of RTC (doesn't work yet)
-Started a new 2D core (doesn't work yet, this version uses old 2D core)
-Added Fold/Unfold option (doesn't work as expected)
-Fixed ITCM (hope it won't break anything)
Enjoy more !!! Mod 3 is out with more fixes !!! This emu is getting better and better !!!
(there is still no linux version...
but this will come soon)
-Added Alpha-test in 3D core, no more color squares around the textures
-Fixed blending in 3D core
-Implemented GXFIFO IRQ : this is a ugly hack but games needing this (ie. New Super Mario Bros) now work
-Fixed depth clearing in 3D core, this fixes black sky bug in Mario64
-Implemented 3D PosTest, this fixes a mini-game in RRR2 (next version will probably feature BoxTest and VecTest)
-Noticeable speed-up, thanks to Shash (now executes 16 instructions at a time)
-Fixed 2 bugs in sound core (loop feature) :
-----Fixed sound length being increased on multiple channel status (key-on) writes
-----Added ability to write Loopstart and Length registers while sound is playing
-----For info : these fixes also fix garbage sound when using "Fold NDS" option
-Added a sound resampling func
-The GUI now uses DirectDraw to display the framebuffer
-----This was hard to implement, but it is WAY faster and better than GDI
-----When you stretch the window, the emu doesn't slow down and the image keeps beautiful (not pixellized)
-----If DirectDraw init fails, the emu will simply use GDI instead
-----DirectDraw is not used when using rotation
-Added CPU low-power mode, this allows RaymanDS to show 3 intros (it is better, but it still doesn't work)
-Fixed 2 bugs in capture unit :
-----Captured bitmap was "invisible" due to alpha values not set.
-----The captured image was only the half of the requested size (128 pixels in width instead of 256)
-----These fixes fix some NSMB/Mario64 mini-games, displaying 3D on both screens (no more flicker, but 3D is still reversed
)
-----Now, DeSmuME is able to pass 4/6 tests (see further posts, NDS graphic test app)
-Added some hacks in VRAM handling, the sprites in NSMB minigames look correct, but now the pause buttons are incorrect
(I plan to rewrite all VRAM handling in next release, current handling is crappy, plenty of TODO and FIXME)
-Wiimote support is not ready, so disabled
-And others...
Download Mods in attachment.
Each rar contains a mod of DeSmuME and its sources.