Currently, the only way to ask for something to be migrated to a site that isn't part of the standard migration path is through a custom mod note.
I currently have two active custom mod notes on Stack Overflow that ask for migration that are not standard targets for SO. I believe the questions could be better answered on another site.
Fortunately, or unfortunately, the questions have been answered, and answers have been up voted and accepted. At this point, a week and a half later, migrating either of the questions would be disruptive to both communities and not necessarily produce a better answer (they've got accepted answers). The unfortunate part is I really do believe that both questions could have gotten better answers and more attention on another site.
What I would like to see is a more streamlined way to flag for moderator attention for migrations.
The UI would look something like this:
This would allow people to find the proper site easily. No more "Migrate this to Mathamatica.SE" because, well, that doesn't exist. Something that I didn't do on this mock up is add a link to the corresponding help/on-topic page for the target site. Something people could check and click before hitting the submit button.
I don't have this quite right again, because while that shows a "closing for off topic", this is a flag and not a vote to close.
The "flag for migration" is only one part of this though. The other part would be to make another flag queue style thingy for moderators in which they could look at just migration flags created through the above interface.
By providing the mods with a "just migration" view into the flags, questions that should be migrated can be quickly identified from the multitude of existing flags and handled promptly before the migration would be disruptive.