This depends on the hardware you are playing on, the version of the emulator and the specific game. I don't have any experience with Prince of Persia games, so cannot make a recommendation. I personally play on RetroArch, which means the PCSX2 core is renamed to LPSX2 and is a little bit lacking behind the standalone emulator. So I would tend to use Dolphin for Gamecube emulation instead. But if you are using standalone emulators, then it might be different story.

When researching the web, people seem to talk about the PS2 versions of the Trilogy being the best. So based on that loose info, I would probably tend to recommend that one. But check out compatibility for each game in the links I gave you.