GUI Tools

Git

Tower - A (commercial) git client with a lot of features making your life easier

Gitkraken - New Git client

MySQL

Sequel Pro - An (open Source) MySQL client

PHPMyAdmin - Open-Source web-based MySQL client

FTP / SFTP / FTPS

Transmit - Commercial FTP client with nice syncing features

Filezilla - Opensource FTP client

Dash

Search (also offline) in API Docs including Joomla ones.

Password management

1Password - Easy to use (Commercial) password manager with integration for all major browsers and iCloud support

Keepass - Open Source password manager

Window Management

Spectacle - Move and Zoom windows around (With Shortcuts - free)

Moom - Move and Zoom windows around (Split view etc. - paid)

Project management / Time

Trello - Card based project task tool

Waffle.io - GitHub driven project management

Time Sink - How much time do you spent in an application

Resuce Time - Cloud based analysis of your application times

Cloud tools

Owncloud - Set up your own private cloud instance

Dropbox

Google Drive

Onedrive

Editors

Atom - Extensible new Editor

Sublime code

TextWrangler