I am torn between two options:
a) having a database with separate games (e.g. in pgn files, or any one of ChessBase, Chess Assistant or SCID database format), where each game would be a subvariation of an opening that I play. This has an advantage for adding verbal annotations, easier printing, etc. This seems also what most professional players, or opening book writers do.
b) A proper opening book in CTG, bin, or whatever other custom opening book format. Possibly one book for my white openings, and one for my Black reperoire. This is better for transpositions, but does not allow me to add verbal annotations - at least not in the formats that I looked at. Chess Position Trainer seems like a good tool for this approach, but still does not let me include variations from database games, so you really can't use it effectively to build a repertoire.
Neither option seems ideal. Any advice?