I feel you on the WPMU -> 3x transition but unfortunately it’s going to be hard to troubleshoot the issues without seeing any code (@sanchothefat says something similar in a comment above). I’ve come up against similiar issues, so let me at least offer some general help in debugging these kinds of things.
Whatever the function in question, go into the SVN and compare code revisions for the function in question. Here’s the WPMU 2.9.2 trunk and here’s 3.0.5.
Try using a diff tool (“diff file1 file2” on the command line) and see what changed between revisions. Are all the parameters the same? Do those array keys exist in both versions?
To slueth out what your code isn’t doing anymore it’s helpful to first figure out it did do that is no longer.