I'm laughing quietly because anyone who sews for their dolls will end up with more outfits than they can possibly store and organize the way you've described. Just a friendly chuckle...
I like to hang my doll dresses up -- I usually keep the slacks, sweaters and tshirts flat in boxes. I often use gallon ziplock bags with a small hole cut in the middle of the folded bottom, then poke the hook of the hanger through the hole and pull the bag down over the dress. It keeps clothes from getting dusty. I do save the boxes and still have some of the original maroon boxes and clothes bags from the early 1990's, but I use them to store things like doll shoes.
I also made a habit of logging everything I buy and make for the dolls onto an Excel worksheet. If you start doing this before you have too much, it's easy to maintain. I set up the worksheet by names of the girls, then list everything that belongs to them and how much each item cost. For clothes I make myself, I include the price of a comparable item. So most of my doll dresses are valued at $18, which is what an AG outfit USED to cost! This helps me to figure out what I need to make (who needs pajamas?) and it's going to be very helpful for the inventory I have to make to include with my will. I can also see at a glance what I've already ordered/own and what I haven't got. Just another way to get organized.