I use plastic tool bins (found at Kmart and Target, Lowes, etc) and they work phenominally for small accessories:
I used to bag everything but it got to be a hassle digging through a box of bags and opening them up whenever I needed to get to them. I like the drawer system much better. Depending on how many accessories you have, it can get expensive though. They cost $8-12 per drawer set. Here's how I've organized my things:
Barrettes: I write the name of the pony the barrette belongs to on a tiny piece of paper and clip the barrette around it. I'll put one or two sets of clips per drawer.
Baby Accessories / Adult accessories: I'll put similar accessories in each drawer (stacking toys in one, big brother hats in another). If they need to be labeled, I use a small piece of acid-free matte tape with the name of the pony on it to tag each accessory.
Brushes/Combs: I sort them by comb style (bear brushes in one, moon combs in another) and I usually only keep one of each shade unless I know it came with a specific pony. Then I tag it with a tape label before putting it in the bin.
Ribbons: Special ribbons (princess, flutter, SHS) are bagged separately and treated like special accessories. Normal ribbons are all together in one drawer. I'll tape lable the ones that I know came with a specific pony.
Ponywear: One outfit per plastic baggie, a couple of baggies per drawer.
Larger accs / Playset accs: I bag and box up baby furniture and playset accessories since they're too big for the drawers.
An excellent guide for baby accessories and ponywear is Lady Twilight's site (greatponies.com). I used that source as well as mylittleponycollector.com and dreamvalley to organize my stuff.