yes... this is the nth program I'm writing in this period. I hope this is the last one :)
Valagtkdoc is a tool that integrates Vala with GTK-Doc for documentation generation.
You can find download and example usage at the homepage.
I think it's far from being perfect, and actually I haven't tried integrating it with autotools, but it shouldn't be that hard. Unfortunately, you have to somehow break the gtk-doc rule "do not run it manually" because valagtkdoc goes in the middle between gtkdoc-scan and gtkdoc-mkdb.
If anybody has a better solution, please tell me :)