What kind of commands do you mean exactly? Commands for admins (which can be typed into the ingame console), or input commands which can be sent to the server process?
About animals: unfortunately they don't respawn yet, so the only way to get new npcs is to use the spawnnpc command, although this only spawns a single animal (so it can be a lot of work to repopulate the world this way)...
Commands for admins can be googled but input commands which can be sent to the server process seem to be no where to be found. These kind of stuff should be stickied.