It appears they are listed in the order you add them. Please add a bug to Bugzilla.
Thanks, -Piers Martijn Anthonissen wrote:
The smart bookmarks used to be listed alphabetically in Epiphany. After upgrading to 1.2.x (Debian packages from the experimental repository), their order has changed, and I am not sure how to rearrange them. Any hints? Thanks, Martijn