ISO

ISO is the disk image format used for games such as Shin Megami Tensei III: Nocturne, Digital Devil Saga: Avatar Tuner, Digital Devil Saga: Avatar Tuner 2, Devil Summoner: Raidou Kuzunoha vs. The Soulless Army, Devil Summoner: Raidou Kuzunoha vs. King Abaddon, Persona 3, Persona 4, Persona 3 Portable. Due to the games being printed on single-layer DVDs, a size limit of 4.7 GB exists for game ISOs.

UltraISO
There are many free programs that edit ISO files. However, a premium version of UltraISO is recommended for its reliablility.

PCSX2
For running the ISO, the PS2 Emulator PCSX2 is suggested. For recommended specs and settings, check this thread.