I store most of my collection in acid free corrugated plastic short boxes from Bags Unlimited. These hold about 100 comics. Their size makes them easy to handle and they should last “forever”.
I also have one 4-drawer legal size filing cabinet I use to store some of my collection.
This is an “OK” storage solution. It should hold about 1600 comics when full. There are a few issues with getting the books to line up (and stay up) though. See these two threads for more info on filing cabinets for comics:
I label the boxes (and drawers) with a BOX ID number that I use to cross reference with Comic Collector so I always know where everything is. The labels on the boxes are held in place using sleeves by Avery (bought at a local Office store) that are designed for CD/DVDs. The labels I design and print using MS Publisher. I usually use rigid photopaper. It makes it easier to slide in and out and looks great with a cover scan. Here is a sample screen-shot of that:
I am slowly switching my collection over from standard polypropylene bags to Mylar Mylite 2s.
I use the “standard” size for most stuff as it fits a variety of eras pretty good. All of the books below are clad in Mylite2 standard size bags: (click for larger)
I buy my bags and boards from E-Gerber.