The N29 gets 18bph on Fri/Sat nights on the inner section (Trafalgar Square - Wood Green). Every third bus goes on to Enfield. On other nights it's 8bph throughout.
I think in terms of passenger numbers it's the 25, but in frequency it's the 38 (28bph AM peak typically, but 35 leave Hackney Central between 7 and 8am). --- old post above --- --- new post below ---
Thinking about your question again, it's quite difficult to do like-for-like comparisons because a lot of the night routes run far further out than their day equivalents - so the N38 operates between Victoria and Clapton, but continues to Leyton and Walthamstow and carries a fair amount of traffic unique to that section of a night. with the N29 it's easier to seperate because so few buses go north of WG on a weekend.
I think the N29 and night 25 are the only routes that run (sometimes) at a higher frequency than their day equivalents, though I'm open to correction on that.
The highest frequency route at any time is the 521. In the busiest hour of the morning peak it has 30 bph. However between the peaks it's far less frequent at only 6bph.
Apologies - I'm out of date (sort of). The 38 will be the most frequent route again since the introduction of the New Bus for London (BorisMaster) next Monday (it's unclear if the new timetable actually came in last week though).