How I've handled this, is I created a unique set of different file folders.
To keep track of a particular batch of beer that I've made, I copy it from one of the recipes under "My Recipes" and then paste it into the "Brewed Beers" folder. So, any batch of beer that I've made in 2013 is in that 2013 folder, with all of my notes, readings, taste notes, things I might want to change the next time I make it, etc., etc.
My base starting point recipe is still in it's original folder. I do put a note in the base starting point recipe of the particular dates that I've brewed that recipe. That way I can go to the "My Recipes" folder and look at the base recipe and then I'll know where to look in the "Brewed Beers" folders for each time I've made it and look at any changes I've made over the years and how they turned out. By having the "dates brewed" in the base starting point recipe, I can quickly and easily find all other "brewed" copies of it to look up my notes, etc.
When I want to make a particular beer that I've made in the past, I'll copy the version that most closely represents what I want to make and paste it into the Brewed Beers folder and then I'll make the changes that I want for this latest brew session to that version only and put in the notes section the reason I wanted to make changes, what changes I made and what I hope those changes will accomplish (more body, drier, sweeter, more or less carbonation, darker, lighter, etc. Whatever I'm trying to accomplish).
As you can probably tell, I'm a note taker and detail oriented. It's probably why I ended up in mechanical engineering for a career.
My files are currently set up as follows:
Note**--The name of each of my files is in "Bold" type.
Scott's Recipes File
Brewed Beers-(Each year is in order by date, with the most recently brewed recipe at the bottom of the list. The recipes in here are basically copies of the Recipes under my other files below, with the readings and notes of the particular brew session in this file by date.)
2010
2011
2012
2013
My Recipes
Ale Recipes
Amber Ales
American Pale Ales
American Black IPA's
Barley Wine
Blonde Ales
Brown Ales
Etc., Etc., Etc.
Lager Recipes-(I don't have lager recipes broken down by style yet, as I have not yet brewed a lager and only have about a dozen lager recipes. I have about 100 different Ale Recipes, so breaking them down by style was necessary to make searching through them easier.)
Award Winning Recipes-(These are recipes that I've found online and in publications that won awards and that I'm interested in making some day.)
Project/Experimental Recipes-(Really weird stuff or something I work on with my Local Homebrew Club.)
Wine Recipes