A new CraftBukkit Recommended Build (1.3.1-R1.0) that provides Minecraft 1.3.1 compatibility is now available.
Important information about this first Recommended Build following a Minecraft update:
The first Recommended Build, as always, is a slightly more polished development build that we're promoting to a Recommended Build so that people who rely on a Recommended Build being available can try out our development builds and decide if they want to use them.
Will plugins break with this build?
Provided the developers of the plugins you are using are keeping up with the development of Bukkit, all your plugins should work fine.