Chaos runes are worth 1 Runespan point and can be used to cross missile platforms. They can also be used to chip nature esshounds. They will disappear and be converted into points if you leave the Runespan.
If you try to bank any runes or essence from Runespan you get the message "A magical force prevents you from banking this item."It is possible to get chaos runes in F2P worlds, if you are siphoning a free-to-play node, and it changes to a Chaotic Cloud.