The Guardian Commander is the commander of choice for:
1) Low economy rushes with level 4 and rocket launchers (Recon should be better for no economy rushes still), often with skirmishers (see pro randy doing Guardian Commander and Ronin recently) while your drone(s) spoof enemy targeting. The heavy drone is particularly obnoxious to deal with. Note that if you really want to, you can get a slightly discounted area shield to go with your GC and make it even harder to do damage to your real units (untested in efficacy).
Strike Commander is also pretty good for a rush, exchanging better hp regen and the ability to get light particle beams and the best heavy weapons for the drones and GCs better skirmishing weaponry.
2) Pushing center and defense creeping
3) Defending against rushes
4) Gaining random scouting every time an enemy unit accidentally paths near your commander and getting free attritional advantage early game
5) There's also the drone spam commander build, which ruins skirmisher's days.
BTW Guardian commander is only 3.5 elmo/s slower than Strike at level 1, which is equivalent to one servo upgrade.