androidterm:
Android Terminal Emulator
http://code.google.com/p/androidterm/

droidbox:
Android Application Sandbox
https://code.google.com/p/droidbox/

TaintDroid:
Realtime Privacy Monitoring on Smartphones
https://github.com/TaintDroid
http://appanalysis.org/index.html

apktool:
A tool for reverse engineering Android apk files
http://code.google.com/p/android-apktool/

smali:
An assembler/disassembler for Android's dex format
https://code.google.com/p/smali/

AndBug:
a debugger targeting the Android platform's Dalvik virtual machine intended for reverse engineers and developers
https://github.com/swdunlop/AndBug

apkinspector:
APKinspector is a powerful GUI tool for analysts to analyze the Android applications.
https://code.google.com/p/apkinspector/

androguard:
Reverse engineering, Malware and goodware analysis of Android applications ... and more (ninja !)
https://code.google.com/p/androguard/

jad:
Java Decompiler tool
http://www.varaneckas.com/jad/

dex2jar:
Tools to work with android .dex and java .class files
http://code.google.com/p/dex2jar/

ded:
Decompiling Android Applications
http://siis.cse.psu.edu/ded/

ARE:
Virtual Machine for Android Reverse Engineering
https://redmine.honeynet.org/projects/are

STOWAWAY:
A static analysis tool and permission map for identifying permission use in Android applications
http://www.android-permissions.org/

COMDROID:
A static analysis tool for identifying application communication-based vulnerabilities.
http://www.comdroid.org/

dex-decomplier:
Dex decompiler
https://code.google.com/p/dex-decomplier/

amatutor:
Android恶意代码分析教程
https://github.com/secmobi/amatutor

mobile sandbox:
Provide an Android application file (apk-file) and the Mobile-Sandbox-System will analyze the file for malicious behaviour.
http://mobilesandbox.org/

apkstatics:
a tool for APK static security check
https://code.google.com/p/apkstatics/

DexGuard:
DexGuard is specialized optimizer and obfuscator for Android
http://www.saikoa.com/dexguard

android-stuff:
This is a repository for random scripts and files using for Android reversing
https://github.com/jlarimer/android-stuff

Dexter:
Dexter is a static android application analysis tool
http://code.google.com/p/android-market-api/

JEB:
The Interactive Android Decompiler.
http://www.android-decompiler.com/

APK_OneClick:

decompile & disassemble APKs

http://forum.xda-developers.com/showthread.php?t=873466

APK IDE:

小米人APK改之理(Apk IDE)是一款可视化的用于修改安卓Apk程序文件的工具

http://bbs.pediy.com/showthread.php?t=168001

ApkToolkit
是一款可视化的用于修改安卓Apk程序文件的工具
http://bbs.pediy.com/showthread.php?t=169975

smali-cfgs:

Smali Flow Graphs
https://code.google.com/p/smali-cfgs/

droidwall:
Android Firewall
https://code.google.com/p/droidwall/

connectbot:
Secure shell (SSH) client for the Android platform

https://code.google.com/p/connectbot/

金山火眼:

在线APK文件扫描及行为分析

https://fireeye.ijinshan.com/

Android安全监测网:
在线监测Android病毒检测
http://www.apk32.com/index.php

Virustotal:
VirusTotal is a free service that analyzes suspicious files and URLs and facilitates the quick detection of viruses, worms, trojans, and all kinds of malware.
https://www.virustotal.com/en/

SandDroid
An APK Analysis Sandbox
http://sanddroid.xjtu.edu.cn/

AndroTotal:
AndroTotal is a free service to scan suspicious APKs against multiple mobile antivirus apps.
http://beta.andrototal.org/

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