I second Sensei's advice concerning changing the bags of newly arrived cels. You never know what type of material those bags are made from, so, better to change it to something that you do know, than leave it in the mysterial material.
Mystery material...I like that
I use polypropelene as well, and I am fortunate enough to live near some Japanese stores that frequently get the bags(I've bought out their supplies every time...). I use the A4L size bags for most standard sized cels, the B4s for standard cels and standard backgrounds, and the B4Ls for those big pan cels and backgrounds that will not fit anything else. I think the largest bags I've seen are the B4Ls, so if you have anything larger than that, you'll have to come up with some origami type way of cutting bags so that they fit. It's particularly fun when you own items that are about 2 feet wide. My advice is that, if you're buying in bulk, buy B4 size bags. Most things can fit in there, and if not, chances are it wouldn't fit in a B4L either.
Oh! If you receive an item with staples in it, carefully take the staples out. The staples are prone to rust and that can damage your artwork. Also, if you're buying sketches, make sure to take the tape off asap. Sensei has great advice on how to do that.
Since I own several types of artwork, I have different methods for keeping each type. For the many backgrounds that I own, I store them in B4 size polypropelene albums that I've picked up at the Japanese store. Each background has its own bag, and since you can fit two per plastic sheet, each folder can hold 40 backgrounds. With cels, I use Itoya folders and let them freely hang.
I, too, have mixed feelings on 'cutting holes' in cel bags to allow them to breathe. I've received perfectly preserved cels that have been in bags with no airation. I personally feel that it depends on how the cel is treated. There are many Japanese collectors who do take really good care of their items, and if you purchase items that were formally in their collections, chances are you'll own a well preserved item. I change the bags on my items every so often, especially when I see wrinkles in the cel bag.