While comptoe.exe is rarely used on its own, it is usually required where pakcompose.exe or sceWork.exe fails to decompress files. A good example is *.unknown files (without the "d" before the dot. The "d" before .unknown probably means "decompressed", so if you don't see the "d", you can try using comptoe.exe.
After unpacking 00016.pak3 with pakcomposer.exe, you have 4 files
00016_0000d.unknown (Battle text, e.g., BLAST CALIBER)
00016_0001d.unknown
00016_0002d.unknown
00016_0003.unknown (Enemy names, compressed)
To edit the enemy names, use the following command to decompress 00016_0003.unknown:
comptoe.exe -d 00016_0003.unknown 00016_0003d.unknown
Edit 00016_0003d.unknown with your favorite hex editor and save as usual
When repacking, make sure to compress 00016_0003d.unknown back to 00016_0003.unknown first: comptoe.exe -c 00016_0003d.unknown 00016_0003.unknown
Once 00016_0003.unknown is compressed again, move 00016_0003d.unknown out of the folder before repacking PAK3 files.