XD I'm also in the "soapcalc recipe in page protector" club! I even scrapbooked a kooky cover for my "cookbook"
Along with the base recipe, I record all the additives that went in, observed time and temperature until gel (yeah I'm a peeker... maybe once I settle on my recipes I'll stop doing that
), any notes about the tracing process, and so on. This has more to do with repeatability than batch lots, but it keeps track of exactly what went into the batch and how it was made. Since pretty much every batch I make right now is different, it's not hard for me to know which bars were which batch... when I start making bigger quantities, I may have to store them with more care to take that into account. (And maybe "born dates" on the labels, too ;D)
As far as ingredients, I've started dating all my supplies with a Sharpie when I get them. I even date my fragrance mixtures when I make them, because especially with essential oils, the mixtures can age to be quite a bit different than the initial throw-together :3
I'm considering soapmaker software when I start trying to sell, because it'd be good to have everything all in one place -- I'm working out of a handful of spreadsheets at the moment.