Fishing Buddy has been updated to work with the most recent patch. I am currently using it again, after having to disable it immediately after the patch hit.
You can get the most recent version (Version 0.9.4m) from WoW Interface here: http://www.wowinterface.com/downloads/info4239-FishingBuddy.html
On a side note, to keep all of your addons up-to-date, I highly recommend jWowUpdater. It will easily update Ace addons, plus you can manually add other addons to update from WoW Interface, Curse and other popular addon sites. Once your addons are on the list, it'll check for an updated version every time you click the "Update" button. Updating all your addons only takes seconds, which makes it easy to stay up-to-date.
You can get jWowUpdater from here: http://code.google.com/p/jwowupdater/ To get it to run properly, you will probably need to update your Java, which you can get here: http://java.sun.com/javase/downloads/index.jsp
Hope this helps!