Boons were introduced in DMG 2 as an alternative to physical treasure. For example: instead of giving a PC a +1 sword, they receive a boon that gives them +1 to their attacks for a reason related to the story of the game. They were designed to either be replaced by an equivalent magic item later, or kept as a permanent ability in lieu of a magic item of equal power and value, and, if they are used in this manner, ought to be treated as such by players, DMs, and judges alike. For example: listed in treasure columns on character sheets, constructed by DMs following rules of balanced rewards, and scrutinized by judges for level appropriateness.
That said, the limiting factor is already inherent in the rules (if they are followed). Boon power should be equivalent to and awarded in lieu of magical items.
Another use for boons, that I've seen on the threads, is in lieu of an artifact. By that, I mean that they are used as a power boost to aid the story for a limited time. In this case they should follow the rules of an artifact. They should only be allowed for a specific time, for a specific purpose. Once that purpose is fulfilled, they move on. I also believe we have a house rule that they are not to 'survive' an adventure thread. I think it also goes without saying that only one of these should be issued at a time (per character at the very most).