When flash is to provide the main exposure for the subject, I prefer to use Standard TTL or Automatic flash mode. All of the balanced fill flash modes—including the ubiquitous TTL BL we have in the digital era—have a tendency to bias the flash output towards underexposure (they are, after all, labeled as "fill flash" or "balanced" modes).
I should point out that each generation of Nikon DSLRs got better at recognizing when it needed to provide subject lighting versus fill, so on a D1 you should always avoid a balanced fill flash mode, but on a D4 and D5 you can often (usually) get away with TTL BL.
If I'm bouncing the flash, I'll usually switch to Automatic flash mode, as I've found it to be a bit more consistent than TTL for large bounces.
