Useful Tools

File System Manipulation

Aaru supports a fairly comprehensive collection of disk image, partition table, and file system formats, and is built with the Microsoft .NET Framework - builds exist, for several operating systems.
kpartx is a fairly standard command to automatically create loop devices for whole disk images (assuming regular partition table types Linux can understand).
macFUSE allows you to use FUSE filesystems on macOS.
OpenVMS ODS-5 file system for Linux is a kernel module, in source form. A TinyCore Linux VM, with it pre-installed is also available.

CBMFS supports various disk image formats (d64, d71, d81, d80, and d82), from 8-bit Commodore systems
Atari 8-bit Utils contains ATRFS, which supports Atari DOS 1, Atari DOS 2.0s, Atari DOS 2.5, MyDOS 4.53, SpartaDOS, Atari DOS 3 (read-only), Atari DOS 4 published by Antic (read-only), and LiteDOS volumes, in ATR disk image files.
FUSEADF supports AmigaOS disk images, and requires ADFLib, to compile.
FUSE-UFS supports FreeBSD UFSv2 volumes.
HFS-FUSE supports Apple HFS+ volumes, including resource forks, and extended attributes.
Acorn ADFS, and DFS implementations, written in Perl. Requires the "Fuse" CPAN module to be installed, to build.
RetroFUSE supports 5th/6th/7th Edition Research UNIX, 2.9BSD, and 2.11BSD file systems
PlayStation 2 Memory Card File System implementation, in FUSE

7-Zip supports the Windows Imaging format (.WIM) disk images, with LZX compression, as used by Windows 8.1.
XADMaster supports a fairly comprehensive collection of compression, and archival formats, and can also expand some disk image formats - this seems to be the basis of the "unar" utility, provided for Ubuntu, and some other Linux distributions.
unshield is a CLI tool, for unpacking various flavours of InstallShield archive.
jSAVF is a Java-based application, for accessing IBM i (AKA OS/400) save files, under Windows, and Linux

The RandomSHX utility, for Windows will extract the contents of some Motorola P2K (e.g. A835) "UNIX Generated SuperFile" firmware archives - this requires Windows, and does not work with UNC paths.
The srecord package, under Ubuntu contains a utility, that can convert Motorola S-Record files, into plain binaries: (for example srec_cat C139_V1.0.03.E.m0 -Output C139_V1.0.03.E.bin -Binary).

BinWalk is extremely useful, for extracting files, and resources out of firmware images, executables, and file system structures.

Dependency Walker for understanding Windows program dependencies and what's used by the program, helpful for software archaeology.
Ghidra is an open-source set of RE tools, including a set of decompilers and disassemblers for most binary formats.

The Amsterdam Compiler Kit is one of the few (mostly) C99 compilers around that can still target a PDP-11 Unix v7 target.
llvm-cbe is the C backend for LLVM -- it can convert LLVM bytecode into C (useful for compiling modern C++ targeting systems that don't have a functional modern C++ compiler, for example).
GNUish Project is a port of UNIX standard utilities for DOS with family mode support (useful for replacing equivalent utilities that cannot be ran under OS/2).