We introduced Oracle SQL Developer to our developers about a year ago. They seem to like it for querying Oracle, but the MySQL connectivity was quirky in previous releases.
Now that Oracle SQL Developer 1.5.4 has been released, I figured I'd give it a try again. I downloaded the software and it started right away with no problem (although I wasn't paying attention and I forgot to migrate over my settings).
Once the software starts, go to Tools > Preferences > Database > Third Party JDBC Drivers and choose the appropriate JAR file.
Then I added a connection with the correct parameters and Voila! I was querying MySQL data from an Oracle tool!