This page is mostly a list of tools I use in my learning process, If I have tried a few ones I will only put the one I preferred.
Decompiler:
Dex 2 jar (Linux/Windows):
Tool to transform Dex file (Dalvik Executable format = Jar for android) to Jar files (Standard Java Archive)
https://github.com/pxb1988/dex2jar
JD-GUI (Linux/Windows/MacOS):
One of the many java decompiler. Possible to use jd-eclipse as ecplise plugin.
Native library executable analysis
IDA freeware for x86/x64 architecture
IDA pro for other architecture
https://www.hex-rays.com/products/ida/
Information Gathering
Website information gathering without direct connections:
Operating systems
Kali Linux (previously BackTrack), Linux version based on Debian including tools for Pen Testing