Pokemon SoulSilver is part of the fourth generation of the franchise, being an enhanced remake of the original Pokemon Silver released in 1999. As such, Pokemon SoulSilver is full of upgrades, showy graphics and new features. It requires a lot of memory to process Pokemon SoulSilver, and emulators like DeSmME (a Nintendo DS emulator of the personal computer) aren't always equipped to handle everything. That being said, there is always something you can do to speed up the processing speed of your Nintendo DS emulator and computer.
Use frameskip. Frameskip is the term used to describe the omitting of certain frames so as to speed up performance. If your emulator is lagging, go to "Menu," "Settings" and then "Frame Rate." Set the frame rate to something lower than it normally is. Frameskipping is not recommended for games that are not otherwise slow. Things will speed up, but the imaging will be of much lower quality.
Edit your sound settings. Sometimes the audio can cause Pokemon SoulSilver to lag, due to the sheer quality that Nintendo has put into the game's sound. Go to "Sound Settings" and set "Interpolation" to "None." Do not use Dual SPU or Advanced SPU Logic in the sound settings menu.
Tweak your computer for optimal performance. SoulSilver requires your computer's full power, RAM and performance. Turn off any "Power Management" settings on your desktop/notebook. Change your computer's power settings to "High Performance." Battery/power settings are usually accessible on the quicklaunch toolbar to the right of the taskbar. Access your computer's Task Manager; for Windows platforms you can do this by pressing Control + Alt + Delete. Close any other programs under the "Programs" tab and any non-vital processes under the "Processes" tab. Last but not least: do not adjust the size of your game's window. Keep SoulSilver's window at a ratio of 1 and leave it alone.
Purchase a new computer if all else fails. Not all computers are built to handle the intense processes of modern Pokemon games. While computers are pricey, new ones come with the most up-to-date graphics, processors, hardware, software and displays.
Don't run DeSmuME on your small notebook (i.e., netbook); it's not designed to play highly text-intensive games like Pokemon SoulSilver. Don't bother upgrading your computer's graphics card; it's usually not the problem. Upgrade your CPU instead. If Pokemon SoulSilver or HeartGold doesn't work out, smaller and less intensive versions (such as Pokemon Silver) usually work without a problem on emulators.
If you are closing the DeSmuME emulator, save your Pokemon SoulSilver game. The program will not save your game by default just because you closed it.