Unimplemented:

A nice GUI
Full hardware reset (reset button only resets CPU)
Gamma
CLK_70
Raster effects (full frame is drawn at SOF instantaneously)
DIP switches
Line interrupts
Beam position
Audio:
 CODEC
 PSGs (partial)
 SIDs
 OPL3
Timing:
 Interval timers
 RTC
VIA0 (cursor->joystick support works, though)
VIA1
NES/SNES ports
PS/2 mouse
Mouse pointer PS/2 input (Pointer itself works)
F256k keyboard
C64 keyboard
UART (RS232 or WiFi)
DMA interrupts
Buzzer (maybe implement with audio? could just ignore it)
F256jr status LEDs
Software reset
Hardware version info
F256k/F256jr machine selection
Integer math coprocessor
CPU selection (6809, 65816)
Upload new flash
Boot from RAM
RAM expansion
Flash expansion

Acceptable lameness: (for now)

CPU: Not cycle accurate. Timing is estimated based on instructions, not cycles.
DMA: occurs instantly, BUSY is always 0
PS/2 keyboard: Output to it is always ACKed and ignored
SPI: Only direct support for SD card commands that the microkernel uses
PRNG: Always gives random numbers, all else ignored. Won't match real thing without cycle exactness anyway.
IEC: not implemented in emulator