Insulating foiled bubble wrap, I buy it by the roll, it's what a the expensive hutch insulation covers are made from but cheaper to buy by the roll. That goes immediately on the outside of the wood, foil side inside to reflect heat, roof included as the roof tends just to be thinner hardboard compared to the walls of the hutch.
I use clear plastic attached to the meshed bits, I have an eyelet punch that I've made a few air holes with and fix these with elastic/cup hooks.
Then the top layer is waterproof fabric, again bought by the roll, I get the heavy duty stuff.
One day I'll make a proper cover which was always the intention but for now it's just wrapped round and fastened down.
I also have some polycarbonate sheets that I use on part of the runs/aviary set up.
Snuggle safes when freezing.