CramFS is a read-only compressed filesystem bundled with Linux 2.3 and later kernel sources.

DouBle provided transparent compression/decompression of Linux block devices. The project is now deceased; an old copy of the software for Linux 1.x is still available at SunSite.

Version 2 of the Journaling Flash File System includes compression support. JFFS/JFFS2 is almost always a better choice than e2compr for flash memory devices, as JFFS provides wear-leveling and e2compr does not. JFFS2 is provided with Linux 2.4 and later kernel sources.

SquashFS is the successor to CramFS, with fewer limitations and better compression.

UPX - the Ultimate Packer for eXecutables
UPX is a transparent decompression encapusulation for executables of various formats. It is the successor to the now-defunct TCX project.

ZLibC provides transparent filesystem-independent zlib (ie. gzip) decompression of data files - but not executables - via encapsulation of GLibC calls.