Here is the problem: .sit archives from 5.5 won't open with Expander 3. You will have to use the same version (or decompress with a higher version) for it to work.
.zip files don't properly handle Mac resource forks and icon database stuff. Don't use zip, especially if you cross the PC barrier. For all my pre-OS X compression, I use CompactPro - it is lightweight, does just as good as StuffIt, and works just fine off a floppy disk. However, StuffIt 5.5 does have useful built in features if you work with a variety of content from all over the place - .zip, .bin, .hqx decoding, etc.
If you can network all your computers with AFP via PhoneNET or Ethernet, then you won't have to worry so much about compression.
.zip files don't properly handle Mac resource forks and icon database stuff. Don't use zip, especially if you cross the PC barrier. For all my pre-OS X compression, I use CompactPro - it is lightweight, does just as good as StuffIt, and works just fine off a floppy disk. However, StuffIt 5.5 does have useful built in features if you work with a variety of content from all over the place - .zip, .bin, .hqx decoding, etc.
If you can network all your computers with AFP via PhoneNET or Ethernet, then you won't have to worry so much about compression.