http://www.mxemu.com/forum/index.php?topic=28635.0
"12) No$GBA is constantly crashing.
While the exact cause is not known, people have attributed it to:
* The "Emulation Speed/LCD Refresh" Setting
* Changing sound modes
* Graphics Drivers (My system doesn't like No$GBA and Catalyst 7.4)"
hope that helps a little.... im not sure if applies to the latest version (2.6) but i hardly play Pokemon at all so i couldn't say from experience :D
EDIT:
these are the optimal settings-
Emulation Speed/LCD Refresh: Unlimited MHz-Disaster, 10%
Reset/Startup Entrypoint: Start Cartridge directly
Video Output: 24bit True Color
GBA Mode: VGA (poppy bright)
GBA Cartridge Backup Media: Auto
NDS Cartridge Backup Media: Flash 512KBytes
Solar Sensor Level: Bright Sunlight
Sound Output Mode: Digital Mono (fast)
Sound Desired Sample Rate: Low (10kHz) (fast)