Hi Chuck,
Those are both good points. I've seen some sites where the help icon is simply replaced with something else (it's in the /images subdirectory), or, less commonly, by an invisible spacer image. It would be nice if DNN allowed better UI replacement in an upgrade-friendly manner, but such is life.
You're right about the "dnn_" controlIds; I noticed them as well. One can actually change this prefix via Default.aspx.vb on or about line 557 to something else without problem. If a one- or two-character prefix is chosen, you actually save a little payload at the same time. No core changes required, but you'll have to propagate the change forward across upgrades.
Same with the forms and anonymous cookies -- can be changed in web.config. I didn't check to see what cookies were associated with the site, so this may have been done already.
Getting rid of the includes in the js/ subdirectory is a little more difficult.
There are all non-visual issues, so I'm not sure about how much Andrew is interested in cleaning them up, but all are good general tips nonetheless.
Brandon