Just as a final postscript to the thread, I was able to use an Autorun.mcl file in the root of the CD-ROM to launch my HTML application successfully. Media Center only pays attention to this file while running fullscreen; if you're running in a window, the normal desktop Autorun.inf takes effect.
Loading time was quite slow, however, since the HTML app brought in a number of Javascript files, style sheets, HTC elements, images, etc - around 5-6 seconds to fully load everything, as the CD-ROM went seek-crazy.
I was able to significantly improve loading time by packing everything into a .mht (Multi-part HTML file), i.e. what you get when you "Save as type Web Archive" from within Internet Explorer. This reduced loading time to about a second.
It's not quite as simple as loading your main HTML page into IE, and doing a Save As. Internet Explorer doesn't properly process HTC references or, indeed, bgsound references for inclusion in the file. However, you can co-erce it to do so by adding some dummy references to the additional files in your main HTML file (I used hidden [img] tags to do this).
I also found it useful to set an explicit background colour in the Autorun.mcl file -- this gives the user some early feedback that something is happening, because the screen changes colour even before the HTML app loads.
Finally, I also noticed that the mere presence of an Autorun.mcl file seems enough to block the automatic scanning of the CD to see if there are any photo or video files to import, even if the Autorun.mcl doesn't point to a real application. This is useful if all you want to do is block the Import requester appearing.