I run several different websites off one installation of MT. These sites all have different domains. However, all of the trackback URLs generated show the domain where MT is installed.
Would it be possible to use something (like symlinks) to make the trackback URLs look like they are from the respective blog's domain?
Reported on Movable Type 4.1x
Yes. You'll have to find out how your host does it, but Apache can be configured to redirect one domain to another. However, it'll ultimately end up at the domain where movable type is installed.
The only problem I foresee is that I don't think Movable Type can be configured to make the values of the Trackback template tags return the domain for the site you want to use instead of the one where Movable Type is installed.