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.
.BNY Binary II wrapped file(s)
.QQ Squeezed file
.BQY Binary II wrapped squeezed file(s) (like .QQ.BNY)
.BNX same as BQY?
.SHK NuFX archive
.SDK NuFX archive containing a single disk image
.BXY Binary II wrapped NuFX archive (like .SHK.BNY or .SDK.BNY)
.SEA GS/OS self-extracting NuFX archive
.BSE Binary II wrapped GS/OS self-extracting archive (like .SEA.BNY)
.BSC BinScii file [use BinScii or GScii]
.BSQ BinScii encoded NuFX archive (like .SHK.BSC or .SDK.BSC) [use BinScii, then ShrinkIt on the output]
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