Binary II wrapper for a file contains ProDOS metadata about file, e.g. file type/auxtype. Binary II is not a compression format, though it can wrap compressed files, including the "squeezed" format supported by BLU (Binary Library Utility) which makes Binary II files.
NuFX is a multifile (archive) format that can contain metadata, compressed files, and disk images.
BinScii is a 6-bit encoding format like Base64.
A Binary II file can contain multiple files; it just concatenates each individual BNY wrapped file within to create an archive. If it's a squeezed file, it ends in .QQ within the Binary II wrapper.
BLU will not make standalone squeezed files, it will only squeeze them when making a Binary II file. You can choose files to be either squeezed or not when making the Binary II file.
ShrinkIt can process all of the above formats except BinSCII.
GS-Shrinkit (aka GSHK) cannot work with 5.25" disk images in NuFX archives.
Nulib2 will also process all of the above formats except BinScii, but it won't unsqueeze a QQ unless it's already inside a Binary II file. 'usq' can unsqueeze a standalone QQ file. 'sciibin' can unencode a BinScii file.
ref:
http://mirrors.apple2.org.za/ftp.gno.org/unix.tools/
http://www.chebucto.ns.ca/Services/PDA/AppleIICompression.shtml