Fish Pond, Abel, and JW Outfitters among others make bags to drool over but they are pricy. I have four of LL Bean's Tackle bags that I use for organizing much of my gear.

I separate my stuff by the type of fishing I do: fly; spinning; Largemouth Bass; Smallmouth Bass; etc. That way I grab the rod(s) I need and the requisite bag and I'm out the door.
[url=http://www.llbean.com/webapp/wcs/stores/servlet/CategoryDisplay?&storeId=1&catalogId=1&langId=-1&categoryId=31649&feat=sr-XS:4e38a]http://www.llbean.com/webapp/wcs/stores/servlet/CategoryDisplay?&storeId=1&catalogId=1&langId=-1&categoryId=31649&feat=sr-XS[/url:4e38a]

If the link doesn't work look on the LL Bean sight under Fishing/Luggage & Gear Bags. The Bean bag has lots of pockets, padded too and removable dividers. It is very similar to the Abel bag but about half the price. It is a great bag for $59.00.