Thanks to http://wakaba.c3.cx/sup/kareha.pl/1256252904/88, here is a security update for Wakaba:
http://wakaba.c3.cx/releases/wakaba_3.0.9.zip
I also disabled XHTML. Times sure do change, huh.
Hopefully I didn't mess anything up, I don't really have a good test setup at the moment. Report bugs and problems!