MapTool 1.3 build 87 lacks support for JAVA 7 at this point. Since that has become the default download, there have been many more error reports with the same information and solution. Here are the steps you can take to make sure you're using the correct version for MapTool.
These problems were fixed in build 88, but other bugs were generated that were more troublesome. Note that you can use both Java 7 and 6 on the same system. You just need to tell MapTool where to look. Thanks for your patience and I expect this will be resolved in the near future.
Update:Apparently Java 7 version 10 has a bug where if used with MT it will not find the JAR file. You currently shouldn't be using Java 7, but if you get that error, this is why.
Update:There is a related thread that discusses the one-click installation of java 6 with no extra configuration needed. Soon this will be moved to the HOWTO section with directions.
viewtopic.php?f=3&t=23237#p237034Update: (4/1/13)
Just noting the latest and last direct links for java 6. I have not tested this with MapTool yet, but I plan to make a 2 minute video showing a fresh install of MapTool. For browser operation, they recommend installing both 32bit and 64bit versions for 64bit systems.