The command you choose is ran after login has occured.  A great example of how to use this is demonstrated using synergy client to connect to a synergy server [Link].

To run a command at startup for Linux Mint 14 (KDE)

1. Menu -> System Settings -> Startup & Shutdown -> Autostart
2. Click: Add Program
3. Type: synergyc 192.168.0.2
   
   * Note, the command in this example connects a syngery client to the host 192.168.0.2.

To run a command at startup for Linux Mint 12 and 13.

1. Menu -> Preferences -> Startup Applications
2. Click Add
3. Give Name: Synergy
4. Command:  synergyc SERVERNAME
   1. where server name is likely your hostname.
5. Comment:

To clarify, things have simplified, and the use of .bashrc or /etc/init.d are discuraged, As per discussion

1. http://forums.linuxmint.com/viewtopic.php?f=90&t=49722