Unix tools are your friends! You can disassemble all files by using a combination of Unix commands. These are easily available on Windows through Cygwin.
find $SYSTEMROOT -name \*.exe -or -name \*.dll -print0 |
xargs -0 -n 1 dumpbin /disasm
The first command finds all .exe and .dll commands. The second applies dumpbin on each found file name. You can redirect the output into a file, or you can modify the above sequence to write the output of each disassembled file into a different output file. You can also replace dumpbin with your favourite disassembler.