Lindsey - Patrick also mentioned putting them on the left. I've seen
evidence to suggest controls work better on the LHS [1] but I'm not
sure if those findings do not apply to mobile development where the
screen size is so much smaller -

Unless you're using a Galaxy Nexus :p  Or a tablet, or just using MobileFrontend in your browser on your fat 50" monitor because you just like the simplicity of the layout.
All - I'll like to see a preferences sub page which does things such
as disabling images. I'd expect in the new look the logo would hint
better that it is a drop down menu and that menu would make sense to
have a settings link which contains these sort of things. The question
is what do we do with them in the mean time? Leaving them in the
footer seems like the obvious choice but it removes a lot of the wow
factor, so maybe putting them in the menu which has yet to be styled
might be more suitable.

I like your sentiment here. Overall I think we should prioritize usability over wow factor - otherwise the wow factor will be overshadowed by usability failure. There's nothing wrong with incrementally wow-ing our users and it will allow us to make adjustments quicker as we get feedback on incremental changes. So my vote is to just leave the links in the footer for now.
Arthur - FWIW (and off topic) I hate that the mobile site link is
right at the bottom of the desktop page. If I'm on a slow
connection/device this is the place i don't want it to be as I have to
scroll to it/wait for content to load. I'd much rather it was at the
top of the page as I can easily flick to mobile where necessary.

I *totally* agree. Regardless, I think the link should be super accessible and super obvious. 

Arthur Richards
Software Engineer, Mobile
IRC: awjr
+1-415-839-6885 x6687