Atari 2600
Acorn Virtual 2600, Atari 2600 Emulator for GBA, Atari VCS Preservation Retrogaming Archive, AtariAge: 2600 Emulation, Dan B's Atari 2600 Tech Page, GP32 Atari 2600 Emulator, Imdylanks Atari Roms, Paul Robson's A26, PCAE, Stella
Atari 5200
AtariAge: 5200 Emulation, Dan B's Atari 5200 Tech Page, Jum52, Vjetnam Atari 8-bit Game Archive, VSX, Xformer
Jaguar 64
JADE: Jaguar 64 Emulation, Jagem (Virtual Jaguar), Jagulator, Project Tempest, Virtual Jaguar GCC/SDL
AtariAge: Beginner's Guide to Emulation
Answers common Atari console emulation questions.
Holme's Atari 8-bit Games
Includes emulators and ROMs for 2600, 5200, 7800, and Lynx platforms.
The Sylvia Project
Multi Atari console emulator for PC, Mac, Playstation and Dreamcast.