Some folks at Berkeley have put together a web site on teaching evolution as a resource for science teachers under creationist assault in the classroom.

Very intersting site. It nice to see information laid out in such an easy to follow manner. Just one problem, they don't really deal with the fact that the current evolution theory (at least how it is taught in schools) doesn't take into account major changes, such as organs (such as lungs), or biological systems (such as sexual reproduction). Do you happen to have a site that can answer those questions?

Actually, it does. See "Looking at Complexity":

http://evolution.berkeley.edu/evosite/evo101/VIICComplexity.shtml

there are additional pages beyond that, too, with discussion of different mechanisms. Intermediate steps is the most obvious mechanism - a light sensor is useful, but a more complex sensor is better, limited focusing even more, etc.

As for schools - even back when I went they said as little as possible to avoid battles with the Creationists, and that was in the '70s.