Turbo Chameleon 64, Flickerfixer, Turbo, REU (and A LOT more) for the Commodore 64
Omnivore is a cross-platform app for modern hardware (running linux, MacOS and Windows) to work with executables or media images of Atari 8-bit, Apple ][+, and other retrocomputer machines and game consoles.
Its goal is to provide all the niceties of modern GUI-based debuggers in a more lightweight and keyboard-friendly package. PuDB allows you to debug code right where you write and test it - in a terminal. Strongly reminiscent of the old-school Turbo IDE for DOS. Syntax highlighting, stack tracing, breakpoints, variable tracking. Cursor key and vi keybindings for cursor movement. Module browser. You can even drop into a Python shell inside the current environment.
The debugger can be controlled from a separate terminal.
A utility for Linux that attaches to a running process and searches the memory field for strings supplied by the user. Once found, you can then change the string to a different value. This works much like the pokefinder utilities on the 8-bit computers.
An open source decompilation application that helps the user reverse engineering applications. Retargetable to different CPUs, so you can (say) reverse a SPARC binary on a PowerPC machine. Modular.
A disassembler for Windows. One of the best in the field, and v2.0 just went beta. It's shareware, though it doesn't appear to lack any functionality if you haven't purchased it yet.
FDBG is a code debugger for code running in user mode (ring 3) in long mode (i.e., 64-bit native mode) on AMD CPUs. Ports for Windows and Linux are available. Written entirely in assembly language, includes source code. Extremely small executable.
BinNavi is a tool for performing static and dynamic reverse engineering of executables for a number of platforms - x86, ARM, PowerPC, and MIPS. Can connect to remote debuggers on other systems to examine running code. Extensible with scripts, can annotate call flow graphs. The source is on Github: https://github.com/google/binnavi
This is a free ebook about using the debugger/hex editor Radare2. It teaches basic techniques for using Radare2 all the way up to reverse engineering 64-bit executables. Free to download.