And some more:
GPGMail / GPGTools: GPG implementation for Mac, including email signing + encryption. Beta for Yosemite currently, but reasonably stable. (I believe it is changing to requiring a payment, though)
Handbrake: for ripping DVDs / converting videos (potentially requires VNC too; I can't remember)
Chicken of the VNC: VNC client
Isolator: for keeping just one window in focus, without using full screen mode
MacTheRipper: DVD ripper
photorec: Unix command line recovery tool, great for recovering photos, documents etc. from USB or memory sticks
Telephone: nice SIP client with address book integration, but does not support encryption :(
Transmission: BitTorrent client, for downloading those Linux distributions