List of known bugs/missing features, 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 on OSX)
ELF encoder may need tweaks to handle OpenBSD
Ia32 compile_c misses many features (divisions, bitfields), and needs a register allocator
Asm parser does not handle well ; comments (eg "foo ; */* blargimdead") (c-style comments are parsed before asm-style, so multiline /* after ; is bad)
The BUGS file is incomplete