Universal rules:
>KO = Either release or box forever
>Blackout is Game Over
>Only catch the first pokemon you encounter on each route
>Nicknaming is mandatory

Here's my set, ORAS specific:
>If you don't nickname (i.e. Spam b to skip through), you can't use the pokemon until you nickname it
This encourages not rushing through the process of the catch
>DexNav is fair game, H O W E V E R: IF you do use the DexNav to catch a pokemon, you must EV train it completely in Super Training until its EVs are maxed out. Failing to do so will render the pokemon unusable until its EVs are maxed out.
DexNav is always controversial in nuzlockes and, most of the time, outright banned. This clause makes it so if you DO use DexNav, you have to prove how invested in that mon you are by EV training it up.
>Shiny Clause: Wild shinies are always allowed in your party
Shinies are an extremely rare case [citation needed], and so, on the off chance that you DO encounter a shiny, you can keep it. Have it in your party at your own risk, though: it will either live or die at your hands.
>No Reviving "dead" pokemon
I know this seems like a no-brainer, but there are some pussies that are too attatched to a mon to lose it or just invested too much time and they wanna bitch about losing it and "revive" it. The whole point of a nuzlocke is for death to be FINAL. If you cared so much, you wouldn't have let it die.

What are your custom rules?