One thing I don't have is a variety of wildcats, but I do have something in just about all of the popular calibers based on the 06' case. From 25 up through 30 caliber. As such, I generally purchase bulk batches of cases in just 30'06 as they are generally cheaper to buy than the specific calibers are. It is then simply a sizing job and to the field I go. Since I generally only load a box of 20 at a time for each of them, it doesn't take long to form them up to add to the stock of other cases when needed.
I mostly just use the Ballistic Tips to keep track of the different calibers in most loads. However on the others with lead tips or straight copper, they all have their own specific labled boxes, and do not get loaded up or taken out to to the range or field together. This helps keep my confusion, as well as anyone elses, down to a minimum. If I am loaning the rifle to someone, I use specific caliber cases. For most shooting however, I can look at the loaded rounds and determine if they go with the particular rifle or not.
Since I only shoot factory rounds in one or two smaller calibers, this never is a problem either.