I know, this thread is a little bit older, but I wanted to share my config for Jak II / Jak III with you, since I feel it might help with some of these problems.
My System:
- Windows 7 Professional 64bit
- 8 GiB RAM (DDR3)
- Intel Core i5 2500k
- Nvidia GTX 570, 2GiB VRAM
I got rid of the black eyes & texture corruptions glitch in Jak II with the following settings (will most probably also work for Jak III and Jak & Daxter). I could not get rid of the weird shadow silhouette thing graphics glitch.
First of all, in your Gsdx settings, set "Renderer" to Direct3d9 or Direct3D11 in Software mode. Notice that this will slow down your emulation a lot. Under "Software Mode Settings" > "Extra Rendering Threads", give the emulator all the extra threads you have left. So if your processor has 4 threads, this should be set to 3. Then, go to your emulator settings and switch to "Speed Hacks". You should set "Emotion Engine (EE) Cyclerate" to 3 and "VU Cycle Stealing" to 2. Also activate "Enable INTC Spin detection", "Enable Wait Loop detection", "mVU flag hack" and "mVU block hack".
With these settings, I can play the game with mostly 60 fps, sometimes it drops for a short amount of time, but I think it should be playable.
I hope, this helps.