You can emulate most of these games released before 2002 with MAME (Multiple Arcade Machine Emulator). Some games (Capcom, SNK) run better on FinalBurn Alpha, Playstation/Namco-based hardware runs better on ZiNc. NAOMI and NAOMI 2 games can be emulated in Demul and/or reicast, with varying compatibility. Nebula also has additional optimization for SNK, Capcom, Konami and PolyGameMaster systems, as well as the Sega Model 2 Emulator, but they haven't been updated in years. For Model 3 games, Supermodel 3 is the only that can do it (for now). For most PC-based arcade games, use Teknoparrot.
Protip: full MAME sets can be found at Pleasuredome and RetroROMS.