If you want to play games at a larger resolution, you may have to explicitly ask Java to use hardware acceleration on some platforms. The following apply to the Sun/Oracle JRE. Check the documentation for the version you are using to see if there is anything more applicable to your setup. Note: In my experience, this can actually cause things to slow to a crawl, especially in Linux with OpenJDK. Your mileage may vary, and in some cases the JVM might already be optimized as best as it can be to suit your platform.
java -jar jace.jar -Dsun.java2d.opengl=true
Or, alternatively in windows you can try activating Direct3D acceleration with the following:
java -jar jace.jar -Dsun.java2d.d3d=true
Because Jace renders into an offscreen buffer and then scales that buffer to the full window, this can drastically improve performance in games that generate a lot of screen updates. Jace is generally smart enough to skip this extra step if there haven't been any changes to the screen in a while, so this setting won't have as much effect if using programs with little or no animation.
Some graphics accelerators work better when scaling the video by whole numbers, coincidentally the result is easier on the eye as well. Press F8 to adjust the aspect ratio of the emulator window.
This emulator is architecturally dependent on threads to manage separate simultaneous operations. Because of this, JACE will always perform better on multi-core machines. When in doubt, make sure your JVM of choice is capable of utilizing your hardware's maximum potential (e.g. use 64-bit if you are running a 64-bit OS).
Disable hardware that is not in use. Storage devices aren't a big deal because they don't do anything unless they are used by the computer, but the super serial card can cause a little bit of drag because it remains active all the time. Also disable the MetaCheat feature if you have no intention of using it. For the most part, though, metacheat will disable more expensive parts of its user interface when the search and heatmap windows are closed.
Also, sound shuts off after a second or two of inactivity. Some games play sounds intermittently and the effect of this starts and stops sound causing emulation lurches. To get past this, increase the "idle cycles before sleep" speaker option. (for example, the default is 2000000, try adding a zero to that). Alternatively, disable sound altogether.