I used the EPU14 Packer in the past alongside the NUKE compression algo. It worked really well for me. I was able to put all of WB1.3 and Extras on a single DD floppy.
http://aminet.net/package/util/pack/epu14You copy the base libs over (really not much needed) and then execute them very early in startup. You have to make sure to leave uncompressed anything that needs to execute, but this isn't much. You can use XPK style compressors like xpkNUKE and you don't even need the large xpkmaster.library file. You only need the following files on the disk in an uncompressed status
DF0:S/Startup-Sequence [variable number of bytes]
DF0:C/EPU [8916 bytes]
DF0:L/EPU1.handler [3496 bytes]
DF0:L/EPU2.handler [10100 bytes]
DF0:L/EPU3.handler [5708 bytes]
DF0:Libs/epu0.library [4192 bytes]
DF0:Libs/epu1.library [1564 bytes]
DF0:Libs/lh.library [2864 bytes]
DF0:Libs/xpkNUKE.library [2900 bytes]
Total: 39740 bytes
Everything else is compressed at over 40% when using a library like NUKE and it's possible that epu1.library and perhaps some of the other numbered handlers may not be required either. This also works on OS 1.x, 2.x and 3.x.
The compression and decompression is completely transparent and you don't need any other files hanging around to decompress anything. You can even place all the files on the disk while the compression flag is enabled and then once it's all set, you boot the disk with compression off and only decompression on. This prevents you from worrying that someone will compress one of the critical startup files.