Tools

This list is a mirror. Original list is maintained here. Feel free to make a pull request to the original list.

General

Good Linux machine or VM either via VMware, VirtualBox, or vagrant - would suggest Ubuntu 14.04 LTS
Python (both 2.7 and 3)
Hex Editor (ghex recommended)

IDA (Demo, if not Pro)
gdb
PEDA - makes gdb far more usable
qira - if you can get it to work & understand it
checksec - peda can give the same info though
pwntools - makes pwning easier
radare2 - reverse engineering framework
angr - a binary analysis framework with a great symbolic execution engine
fupy - fast and dirty python decompiler
JD-GUI - java decompiler
Java Decompilers - Online decompiler for Java and Android APKs
syms2elf - A plugin for Hex-Ray’s IDA Pro and radare2 to export the symbols recognized to the ELF symbol table

Rumkin ciphers - multiple (ancient) crypto stuff
quipqiup - solving cryptograms
xortool - solving multi-byte xor cipher
rsatool - to calculate rsa params
featherduster - An automated, modular cryptanalysis tool
attackrsa - An all-in-one tool including many common attacks against RSA problems in CTF
RsaCTFtool - An automated tool to crack public keys of rsa using various standard techniques
Untwister - A seed recovery tool for various PRNGs

Foremost - recover hidden files
Binwalk - find offsets of files which are concatenated contiguously
Autopsy - find deleted files from harddisk dumps
Wireshark - analyze network captures
Stegsolve
Cloudshark - Analyze network captures online
John The Ripper - password cracking tool
Stegosaurus - tool that allows embedding arbitrary payloads in Python bytecode (pyc or pyo) files