I was able to get around this bug by specifying the following in my .Xdefaults file:
Emacs.FontBackend: xft Emacs.font: Consolas-7.5
Then doing xrdb -load .Xdefaults.
(Beware, xrdb seems to silently discard the last line of the file if you don't terminate it with a newline.)
This gets me the desired behavior on new frames. Emacs is the only program out of the half dozen I regularly use that was unable to specify its own font. In fact, it is the only program I have _ever_ used that falls into that set. I'm sure there are very good explanations and/or historical reasons for this, but it's a serious pain point.
Another data point: I originally observed this problem on an emacs matching with the following version string:
GNU Emacs 22.214.171.124 (i686-pc-linux-gnu, GTK+ Version 2.12.0) of 2008-06-16
This is the emacs I checked out from CVS yesterday.
I have another emacs with the following version string:
GNU Emacs 126.96.36.199 (x86_64-unknown-linux-gnu, GTK+ Version 2.8.20) of 2008-05-15
If I use this emacs on my desktop workstation, I have no issues with new frames and fonts. But if I use the same source, compile it, and load it on my laptop (the same machine on which I originally encountered the bug), I have the bug. This convinces me that there is some interaction between emacs and my computer that is present on one machine but absent on the other that is causing this issue.
I've checked xrdb and there's nothing to explain the problem there. I have no manually set fonts in either except when my workaround is active. I don't know where else to look, but I do have two machines to diff if you guys have some suggestions or things you would like me to copy.