I agree with nephilim....
http://freshmeat.net is awesome.
I personally like the CLI but I will try to include GUI apps as well.
IRC
* XChat (GUI)
* BitchX (CLI)
FTP Client
* gFTP (GUI)
* NCFTP (CLI)
Network Scanning software
* nmap (CLI) - This is the defacto network scanner IMO. You may find some apps which couple a GUI to it on freshmeat.
Photo Editing software like Photoshop
* GIMP
SSH
* errr... $~ ssh.