I suggest you check out the following product, it will help you do what you are asking..
Atari Running on Any MachineIt's very reminiscent of Amiga's own UAE emulator, but it's designed for people who aren't so much wanting to emulate old hardware as to have a solution for running GEM on a PC and it works well with well behaved TOS/GEM programs and brings that platform into the age of current machines (it runs DivX and supports way better graphics and speed than any old gem/atari machine could,.
Official features are:
MC68040 compatible CPU (including optional MMU!)
MC68881 compatible FPU
JIT Compiler for CPU and FPU (speeds up CPU+FPU up to 10x!)
ST-RAM 14 MB
Fast-RAM configurable 0-3824 MB
Host accelerated fVDI graphics (large highcolor/truecolor resolutions)
Access to Host OS filesystems using BetaDOS or MiNT native XFS driver
Ethernet networking via host using MiNT-Net XIF driver
TOS 4.x XBIOS compatible sound (16-bit 48 kHz stereo sound)
Parallel port (bidirectional)
MFP, IKBD, ACIA, VIDEL, BLITTER, FDC, IDE, DSP MC56001
Please note although these features sound great it's not an attempt to emulate any previous atari machine.
Here are some screen shots:
