Comment by rdl

The main constraint is budgetary authority; it's easier to create a new secret program than to fund it. Ultimately all funding authority comes from the US Congress, although there are layers of obfuscation.

The ability to create new Special Access Programs is usually delegated to the level in an organization that actually does this routinely; definitely below Department level, above Combatant Command level.

On the Army side, check out AR 380-381, and legally, 32cfr159a. Basically someone more operational creates it, and then gets approval from above, but the authority to create the program is closer to the action than the ability to finance it.

They deconflict on names at one level, usually per department (e.g. Army, Navy). I think this is done by pre-assigning names in batches to be used. http://en.wikipedia.org/wiki/CIA_cryptonym is an interesting article.