Scratch that for vim, it works after I installed vim-python and "set
mouse=a". :)

I believe that the other applications are the result of vte no longer
sending arrow up/down keypresses when using a mouse wheel, since those
applications do not actually have mouse wheel support built-in. This is
apparently called "alternate screen scroll" and the following bug report
for vte has a patch for vte and gnome-terminal that makes the feature
toggleable:

http://bugzilla.gnome.org/show_bug.cgi?id=518405

This patch appears to have been accepted into vte for intrepid, per:

https://bugs.launchpad.net/ubuntu/+source/vte/+bug/106995

-- 
Mouse scrolling does not work in vim, mutt etc.
https://bugs.launchpad.net/bugs/291184
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