WordPress 3.0.4 was released a few hours ago to fix a couple of persistent XSS vulnerabilities. One of these was discovered by me, and I also participated in lengthy discussions about the fix (maybe more on this at a later date). It is strongly recommended that you update now as this is a critical security release.
I have just pushed an update to Exploit Scanner with a new set of hashes for WordPress 3.0.4. The update also removes the wp-content folder and sub-directories/files from the list of core file hashes. This was done because of the difference in the release cycles of WordPress and Akismet; Akismet 2.4.0 got included in the 3.0.4 package, however 2.5.1 is the current stable version (hopefully this will be addressed by a change in core in the future, maybe either dropping it from the package and/or never touching wp-content on updates only initial installs).
I plan on releasing the next ‘major’ version of Exploit Scanner to coincide with the release of 3.1. The main new feature, which has actually been sitting in trunk for quite a while, will be core file diffs. This will allow you to see exactly what has changed if the plugin detects a modified core WordPress file. Please download the development version and give it some thorough testing if you feel like trying out the new goodness.