If your team comp consist of a mid who has TP already, consider taking ignite into bruisers or even tanks like Cho'Gath to secure your ultimate.
Against assassin tops such as Akali and Bruisers such as Irelia, Camille, Jax you might want to take exhaust into the match up to prevent them from all ins as well as providing more damage when you hit your ulti for an all in.
These are the perfect runes for Urgot this current patch. Here are some tips on what to do with the active runes.
Spellbook: Take ignite level 6 to secure your kill in lane. Remember you can ignite and then press ulti so that the second the enemy Top laner is under 25% he is a free kill for you. Later stages running exhaust for adc in teamfight. Spellbook is the perfect rune for smart players are they can utilise the summoner spells to bait players as well as making unexpected plays.
Perfect Timming: Simply to prevent and trade aggro on tower dives. A little trick with urgot is that you can use your ultimate, press stop watch and if there is aggro on the champ say for example a tower. The ultimate will go through as usual even though your in zhonyas.
Minion dematerializer: Use this to shove waves and secure cannons.