My answer would depend on the complexity of your configuration.
If you're planning an extensive multi-panel UI with dozens of options on each panel -- for example, Grid's config UI -- then I'd suggest using AceConfig or, if you're a serious masochist, AceGUI directly.
If you're planning a single panel, I'd suggest just writing it yourself using Blizzard templates (see
PetBattleAutoForfeit for an example).
If you're planning a few panels with a few options each, I'd suggest either writing it yourself using Blizzard templates, or using some mini-libs to simplify generating the widgets, like tekKonfig (see
StealYourCarbon or some of Tekkub's other addons) or PhanxConfig (see
ShieldsUp for an example).