I didn't go into much detail in my arcade thread, as it was more about the build, but obviously Im doing a shit load of emulation on it.
I'm using Libretro (http://www.libretro.com/
) which is running Retro Arch as the front end interface. Which in turn is running through EmulationStation (http://www.emulationstation.org/
) which is a graphical front end for all your emulators and ROMs.
EmulationStation is available for windows, so maybe you should give it a try to get everything sorted in once place.
My arcade has libretro cores for emulators for Atari all the way to Dreamcast. I still have shit load of emulators to configure properly, like MAME, and loads of old colour PC's but everything works pretty good for now.
Yeah I hear PCSX2 is pretty good these days. Especially if you got some good hardware. I would have to recommend PPSSPP (http://ppsspp.org/
) which is like the best PSP emulator for PC. It plays loads of titles, supports multiplayer, HD, and heaps of options for texture scaling and such. Pretty much allows PSP games to run at their best without the limits of PSP hardware.
Also if you want to play Jak and Daxter etc. It may just be worth getting an old PS3. They are silly cheap on places like trademe these days. Then you can just buy all the HD collections for balls cheap for Jak and Daxter and such. You spend enough on games like me :P Which is probably enough reason not to do it, as it is to do it.