Even though, as you already know, most of the changes are going to be internal, here is a really visible one:
All addresses will change from https://www.bugtrack.net/secure/ to https://mycompany.bugtrack.net/ and you will need to update all URLs.
We tried to make migration process as seamless as possible for users. If users will attempt to access an old address (either by following the bookmark, or a saved URL, say from an old e-mail notification message), they will be presented with the address change notification banner and after a short delay redirected to a new location.
BUGtrack Professional Edition administrators should check automation services they currently use to update to the new address scheme.