Frodo is a free, portable C64 emulator. It focuses on the exact reproduction of graphical effects possible on the C64, and comes in three "flavors" (Frodo, Frodo PC, and Frodo SC) with increasingly higher quality of emulation, but at the cost of higher processing power requirements. Frodo has been ported to a number of systems, including handheld computers. The Unix version can use either SDL, X11, or SVGAlib to display the graphics.
KEGS is an actively-developed Apple IIgs emulator, originally written for HP workstations, improved and customized for Linux. It runs under X at any display depth, and supports changable memory sizes, joysticks, and sound. KEGS boots all Apple II OS variants, and supports all of the graphics modes of the Apple IIgs. It requires a copy of the Apple II system ROMs. Kegs has been adapted to work under Mac OS X, Windows, and the SDL library.
The MMX Emulator library provides a simple way to (slowly) execute binaries that use MMX instructions, on processors that do not support them. It can be used if you want to develop MMX code, or execute MMX binaries, on a non-MMX Intel compatible CPU. Please note that well written MMX binaries should contain the equivalent non-MMX code, since the emulation will always be really slow, and MMX code is all about speed.
PCEmu is a software-only PC emulator that emulates an XT- class machine with text-only VGA. It supports hard and floppy drive images, and allows mounting of Unix directory trees as drives. An EMS interface allows access to arbitrary amounts of memory. It also has a DEBUG-style hardware debugger.