Backing up Freenet
There are various files and folders to backup for different parts of Freenet. Most of them include a number, e.g. node-24374. The number is usually the node's darknet port number - you can see this at the bottom of the Friends page for example. Below we just say node-*.
Settings and peers
You need to backup your node-* and peers-* files to keep your darknet peers. When restoring you need to make sure the node keeps the same darknet port. The best way to do this is probably to backup your freenet.ini as well. It might be a good idea to also backup your opennet (= strangers networking) data: opennet-* openpeers-* and openpeers-old-* (note that the number for these is your opennet port number, it is different than the number for everything else).
Queued downloads/uploads
You can backup your downloads and uploads by backing up the node.db4o and persistent-temp-* files. Again you should keep the same darknet port number.
Datastore
Your datastore is probably too big to backup, but if you do want to back it up, it's all in the datastore folder.