List of known bugs/missing featurs, in no particular order:

PPC cpu cannot parse/encode code
Disassembler is sloooow
The GTK UI is quite sluggish too
Disassembler backtracker does weird things
Mach-O encoder does not work (binaries won't load)
Ia32 compile_c misses many features (division, bitfields), and really needs a register allocator
The BUGS file is incomplete