One recurring theme is elJefesLoophole (in summary a flaw in the rules that allows anyone to change the rules). This has been done to death, and in some senses the correct thing to do if you discover this loophole is to use it to fix itself. - WildCard
Another matter that seems to often arise early in the life of a Nomic based on Suber's initial ruleset (or anything with a similar concept of proposed rule changes) is that of bribery. Inevitably someone who foresees difficulty getting enough votes for a new rule will add a clause to the proposal that rewards those who vote for that proposal (or penalises those who vote against it). This tends to provoke both outrage and imitation. The obvious solution is a rule that forbids such bribery; does anyone know of a Nomic where this issue came up and was resolved in some other way? (See NomicWorldSummaryI for an account of this theme occurring in a particular game.)
Another theme is creating some sort of board on which the game is played.