Clements said:
You are using the default, and looking at those specs, turn on both Anti-aliasing and Anisotrophic filtering for improved picture quality (I'm sure the Radeon can more than handle it!) and turn the resolution up to maximum. That should improve the crispness of the graphics.
Or you can do same as I do, use the default setting when in window mode and you can also watch TV
Or use the default settings also in full screen mode.
Note: since you have the best All in Wonder card on the market, you can try something very deferent, start PJ64 and load a ROM in window mode, then pause PJ64 with the F2 key, start the TV program also in window mode, right click on the TV and select ThruView Desktop, and make sure that PJ64 full screen res is the same as you desktop, then hit F2 resume and hit Esc to goto full screen and, there is something very deferent.