I have most of my stuff packed into Rubbermaid Roughneck storage totes (18gal size). I have them organized as follows:
1) all eating dishes/utensils
1a) all cooking dishes/utensils (these two may be the same container, I don't actually remember, lol)
2) all non-perishable food
3) equipment that gets totally unpacked every trip (lantern, tablecloth, etc)
4) equipment that may or may not get used every trip (hammocks, clothesline, etc)
5) supplies (things that need replenishment as the season goes on)
I got the tip about the clothes from a post on here a while ago. It's great! It doubles as a table in the tent also. I have the King Pine from LLBean, and use one of the empty containers in the screen house part of the tent for anything we want to keep in there but don't want it to get wet. It usually gets pulled out to double as a table for the campfire too.
I love these containers. They hold a lot and I can easily handle packing them in and out of the car. They also stack nicely in the screen house (I have one seperate from the tent).
Large soft duffels by companies like Jansport and many others. They are as big as the plastic bins, but don't scratch the inside of your vehicle and fold flat when not in use. Oh yeah, and some like the Jansport brand carry lifetime guarantees.