Here are my top 5
No-one's reading this far, I know....
Best editor bar none, blazingly fast, I use vim for almost every application of reading or writing text. This is a Pragmatic Programmer tip: Use a Single Editor Well.
I've nothing against emacs, but those nancy boy IDE editors (Kate, gedit, Eclipse et al) are like toy things compared to vim or emacs, once you have several years experience.
The swiss army knife of media operations. Can do almost anything to almost anything. Used as a base for mplayer, vlc, whole host of other media libraries, the command line tool can do anything those can do.
A general purpose programming and scripting language for the 21st century. Begone with your bash scripts.
A fast browser that looks decent, is regularly updated, doesn't leak memory all over the shop (hi Firefox).
moc - music on console - is a background music player that you run from your console. You can detach from the player, and it continues on running, and is instantly available from any shell, eg from vim, :!mocp
mpd - music player daemon - is a networked background music player. You run the server on one box, and connect clients from another box. You can also push the audio output from the server through icecast, and broadcast over rtmp to your lan.
I assume all of these things are available for Linux, they certainly are for FreeBSD.