My personal preference is Eclipse (with various plug-ins) as I am developing in several languages (PHP, Java, and Ruby) and this way I am always used to interface and keyboard shortcuts. This is not a minor thing as you become very productive this way.
I haven't used Aptana, but will (hopefully) soon - it does look interesting, though.
For others IDEs I have used: jEdit (for little Java), Notepad++ (still for some scripting and short test code runs).
And for the features You asked: Eclipse support many source code version servers (Subclipse); your project can be on a Samba share; ZendDebugger/xdebug for debugging.