I'd like to see Channel F as well, the MAME/MESS cores can do it, an early system important for historical purposes. Also, RCA Studio II for the same reason.
As a Mac user since 1988, I'd love to see MiniVMac added, fun to show people the games with 1-bit graphics, lol. Basilisk II (color Mac II) would be even better!
I know this has been mentioned a bunch, but Daphne the Laser Disc Arcade Game Emulator would be great! The most popular two (Dragon's Lair & Space Ace) have received ports to other systems like Sega CD & Wii but there's a bunch of other Laser Disc based games that I don't think are playable any way other than Daphne.
PinMAME? VPinball? Not sure if that's workable on Linux, but I just mounted side "Flipper" buttons on my cabinet for Pinball games!
Also, Standalone emulators Stella (Atari 2600) and Standalone MAME, would be great! Reasons being that the RetroArch cores based on Stella do not have Mouse/Trackball/Spinner support for some reason but the standalone does, and Retroarc in general has an as-yet unresolved issue with Mouse/Trackball/Spinners where the hidden mouse loses focus on the Retroarch window causing the mouse to stop working at random locations in-game (as if it's hitting an invisible wall).