Command+Shift+F to find a string in your project.
Command+Shift+V to view paste and clipboard history
Command+, to open the preferences tool
Command+1 to toggle side bar

Double Click Shift to search all files
Command+O to find a class
⌘⌥O to find a symbol or function (useful for searching for php or javascript functions)
Command+Shift+O to find a file in your project.

Command+K to Commit a change to git (you need to run a git init in your project folder first though for this to work).
Control+Tab to switch views such as the projects folder or the built in terminal.
Option+Command+T to surround a block with a new directive such as a an if statement.
Command+N to create a new file
In your PHP preferences you can set the file and code templates for when each new object is created.
Command+arrowUp to open a floating project navigator.
Command+E to view recent files.
Command + Option + Z to rollback changes since last commit.
⌥⇧⌘F on the database to search for any string in the database.
Command + Option + L to for a json into a more readable format (on a json scratch file)
/** then enter to fill out function comments.
Command + N to create a new scratch file
Command + Enter on a mysql or sql create a sql query on the database