Minecraft 1.6.x will be released shortly, here is a list of FAQ'S that will help you through the update process:
Q: When I try to connect to my server it says it is outdated, what do I do?
A: Follow this guide and update to Minecraft 1.6.x Official.
Q: Will updating my server to Official Minecraft disable my craftbukkit plugins?
A: Yes, after you update your server using the guide above craftbukkit and all craftbukkit plugins will be disabled.
Q: When can I get my plugins back?
A: When the craftbukkit team releases a stable build for Minecraft 1.6.x
Q: When will Craftbukkit be updated for the new 1.6.x release?
A: We do not know. As soon as they do we will make an announcement on our website. Also feel free to keep an eye out for news from the Bukkit website here: http://bukkit.org/
Q: But I need Craftbukkit on my server I can't run my server without it, what do I do?
A: If you absolutely need craftbukkit for your server at all times your best option will be to not update your server until the craftbukkit team releases a new version for 1.6.x If you choose to wait DO NOT update your minecraft client on your computer to 1.6.x You will also have to tell your players not to update.
Q: I already updated to Official Minecraft 1.6.x but I need to go back to Craftbukkit for 1.6.2
A: Follow this guide to revert to the 1.6.2 craftbukkit beta build: http://www.minecraftserverhost.net/secure/knowledgebase.php?action=displayarticle&id=142
Q: Should I backup my map before updating?
A: That is up to you. However if you rely on plugins for map protection then we would highly advise backing up your map before updating.
Q: Will all my plugins work when the new craftbukkit release for 1.6.x comes out?
A: It's about 50/50. Your best bet is to disable any plugins that are outdated when the craftbukkit 1.6.x release comes out. You will want to wait until the plugin authors update the plugins you are using and then you can update or re-install them.
Q: How long will it take for my plugins to be updated?
A: We do not know. Updates are done by individual authors, some authors update quickly, while others take weeks or months, some plugins go inactive after a new craftbukkit release.