When you are using npm, bower, and git behind a proxy server you have to do a little bit of configuration. Luckily it is super easy to do these configurations. Almost all of the programs have command line commands to set and unset the proxy server.
Updates:
Updated 2015-Feb-01: Added running source command for Bash and Ruby Gems section
Updated 2015-May-07: Added the Ionic Start command
Updated 2015-May-08: Added the Android SDK
Updated 2015-Aug-03: Added command lines to set proxy
Updated 2015-Oct-20: Added Gradle
Windows Command Prompt
Current Command Prompt Only
set http_proxy=[Your Proxy]:[Proxy Port]
set https_proxy=[Your Proxy]:[Proxy Port]