Disassemblers, debuggers, and other static and dynamic analysis tools.

https://github.com/angr/angr

 - Platform-agnostic binary analysis framework developed at UCSB's Seclab.

https://github.com/bwall/bamfdetect

 - Identifies and extracts information from bots and other malware.

https://github.com/BinaryAnalysisPlatform/bap

 - Multiplatform and open source (MIT) binary analysis framework developed at CMU's Cylab.

https://github.com/programa-stic/barf-project

 - Multiplatform, open source Binary Analysis and Reverse engineering Framework.

https://github.com/google/binnavi

 - Binary analysis IDE for reverse engineering based on graph visualization.

https://binary.ninja/Binary ninja

 - A reversing engineering platform that is an alternative to IDA.

https://github.com/devttys0/binwalk

 - Firmware analysis tool.

https://github.com/aquynh/capstone

 - Disassembly framework for binary analysis and reversing, with support for many architectures and bindings in several languages.

https://github.com/hugsy/codebro

 - Web based code browser using  clang to provide basic code analysis.

https://github.com/radareorg/cutter

 - GUI for Radare2.

https://github.com/sycurelab/DECAF
DECAF (Dynamic Executable Code Analysis Framework)

 - A binary analysis platform based   on QEMU. DroidScope is now an extension to DECAF.

https://github.com/0xd4d/dnSpy

 - .NET assembly editor, decompiler and debugger.

https://www.jetbrains.com/decompiler/dotPeek

 - Free .NET Decompiler and Assembly Browser.

http://codef00.com/projects#debugger
Evan's Debugger (EDB)

 - A modular debugger with a Qt GUI.

https://github.com/rabbitstack/fibratus

 - Tool for exploration and tracing of the Windows kernel.

https://www.mcafee.com/us/downloads/free-tools/fport.aspx

 - Reports open TCP/IP and UDP ports in a live system and maps them to the owning application.

http://www.sourceware.org/gdb/GDB

 - The GNU debugger.

https://github.com/hugsy/gef

 - GDB Enhanced Features, for exploiters and reverse engineers.

https://github.com/NationalSecurityAgency/ghidra

 - A software reverse engineering (SRE) framework created and maintained by the National Security Agency Research Directorate.

https://github.com/codypierce/hackers-grep

 - A utility to search for strings in PE executables including imports, exports, and debug symbols.

https://www.hopperapp.com/Hopper

 - The macOS and Linux Disassembler.

https://www.hex-rays.com/products/ida/index.shtml

 - IDA Pro Windows disassembler and debugger, with a free evaluation version 

https://github.com/crypto2011/IDR

 - Interactive Delphi Reconstructor is a decompiler of Delphi executable files and dynamic libraries.

http://debugger.immunityinc.com/Immunity Debugger

 - Debugger for malware analysis and more, with a Python API.

http://ilspy.net/ILSpy

 - ILSpy is the open-source .NET assembly browser and decompiler.

http://kaitai.io/Kaitai Struct

 - DSL for file formats / network protocols / data structures reverse engineering and dissection, with code generation for C++, C#, Java, JavaScript, Perl, PHP, Python, Ruby.

https://lief.quarkslab.com/LIEF

 - LIEF provides a cross-platform library to parse, modify and abstract ELF, PE and MachO formats.

http://ltrace.org/ltrace

 - Dynamic analysis for Linux executables.

https://github.com/phdphuc/mac-a-mal

 - An automated framework for mac malware hunting.

https://en.wikipedia.org/wiki/Objdump

 - Part of GNU binutils, for static analysis of Linux binaries.

http://www.ollydbg.de/OllyDbg

 - An assembly-level debugger for Windows executables.

https://github.com/moyix/panda

 - Platform for Architecture-Neutral Dynamic Analysis.

https://github.com/longld/pedaPEDA

 - Python Exploit Development Assistance for GDB, an enhanced display with added commands.

https://winitor.com/pestudio

 - Perform static analysis of Windows executables.

https://github.com/cmu-sei/pharos

 - The Pharos binary analysis framework can be used to perform automated static analysis of binaries.

https://github.com/plasma-disassembler/plasma

 - Interactive disassembler for x86/ARM/MIPS.

https://www.mzrst.com/

 - A Professional PE file Explorer for reversers, malware researchers and those who want to statically inspect PE files in more detail.

https://docs.microsoft.com/en-us/sysinternals/downloads/process-explorer

Process Explorer Advanced task manager for Windows.

http://processhacker.sourceforge.net/Process Hacker

 - Tool that monitors system resources.

https://docs.microsoft.com/en-us/sysinternals/downloads/procmon

Process Monitor - Advanced monitoring tool for Windows programs.

https://docs.microsoft.com/en-us/sysinternals/downloads/pstools

 - Windows command-line tools that help manage and investigate live systems.

https://github.com/joxeankoret/pyew

 - Python tool for malware analysis.

https://github.com/Cisco-Talos/pyrebox

 - Python scriptable reverse engineering sandbox by the Talos team at Cisco.

https://github.com/ispras/qemu/releases/QKD

 - QEMU with embedded WinDbg server for stealth debugging.

http://www.radare.org/r/Radare2

 - Reverse engineering framework, with debugger support.

https://sourceforge.net/projects/regshot

 - Registry compare utility that compares snapshots.

https://retdec.com/RetDec

 - Retargetable machine-code decompiler with an 

https://retdec.com/decompilation/online decompilation service

 and 

https://retdec.com/api/API

 that you can use in your tools.

https://github.com/Cisco-Talos/ROPMEMU

 - A framework to analyze, dissect and decompile complex code-reuse attacks.

https://github.com/pidydx/SMRT

 - Sublime Malware Research Tool, a plugin for Sublime 3 to aid with malware analyis.

https://sourceforge.net/projects/strace/strace

 - Dynamic analysis for Linux executables.

https://triton.quarkslab.com/Triton

 - A dynamic binary analysis (DBA) framework.

https://github.com/vmt/udis86

 - Disassembler library and tool for x86 and x86_64.

https://github.com/vivisect/vivisect

 - Python tool for malware analysis.

https://developer.microsoft.com/en-us/windows/hardware/download-windbg

 - multipurpose debugger for the Microsoft Windows computer operating system, used to debug user mode applications, device drivers, and the kernel-mode memory dumps.

https://github.com/x64dbg/X64dbg

 - An open-source x64/x32 debugger for windows.