Actually, you can use C:GDBStub and C:GDBStop from the aros-m68k-system.iso from the aros.org download section. Make sure to get the ISO - it's in AOS HUNK format. The tarball is for debugging AROS itself, and is in ELF format.
It runs on not only AROS, but also KS 1.3 ... KS 3.x, and uses the serial port for the debug port.
C:GDBStub is a self-detaching program, and installs hooks into Exec/Alert(), the TRAP vectors, and every newly run program's default tc_TrapHook. When those hooks trigger, it starts up a GDB Stub target on the serial port.
(You can use C:GDBStop to start a GDB Stub session manually)
I don't use WinUAE myself (I'm on Linux), but I think Toni might have a TCP serial port option in the latest Beta series.
You can then use a m68k-elf-gdb on your host with the 'target remote localhost:1234' command to make a local connection to the emulator's serial port.
NOTE: When using C:GDBStop, you'll need to 'set $pc=$pc+2' to skip over the 'trap #1' instruction before continuing execution.
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