My freezer is a disaster. I usually try to keep similar things together on each shelf - one shelf for veggies, one for fruits, one for proteins, etc. When I get to the point where I have no idea what's in my freezer, I know it's time to reorganize. I think things started to go downhill when my husband left a bottle of champagne in the freezer to chill, which then exploded. The freezer was torn apart to clean up glass shards, and hasn't been the same since.
One of my favorite tips for organizing the freezer is this - wear winter gloves! It becomes painful to handle frozen items with bare hands after about the first minute. I accidentally came across this idea one winter, when I came in from grocery shopping, and kept my gloves on while unpacking my groceries. I thought to myself...why don't I keep my gloves on every time I'm moving things around in the freezer?
Give it a try. You might find yourself organizing your freezer more than once every 5 years.