There are three places where publishers are recorded:
A - Publisher field on the Cover Title - only one publisher may be selected
B - Title Description on the Cover Title - since this is free text, anything may be entered
C - Publishers field on individual issues - multiple publishers may be selected here

What goes in each place for the variety of imprint books like Vertigo or Homage?
A - The "most prominent" publisher. For most imprint books, this should be the imprint itself, such as Vertigo.
B - All significant publishers. For Vertigo books, this would be Vertigo and DC.
C - Every publisher associated with a single issue

How do we select which publisher to use for books which moved from publisher to publisher over the years, like Uncle Scrooge or Turok?
A - The "most prominent" publisher. For books that migrated over the years, this may be a judgement call. If the book is current, generally use the current publisher. If the book has ended its run, the longest running publisher may be more prominent.
B - All significant publishers, as is done now on Walt Disney's Comics and Stories.
C - Every publisher associated with a single issue

In a similar case, what about Imprints that moved from publisher to publisher, like WildStorm? Some books in the run may have been published by Image, some by DC, and all may have WildStorm attached to them.
A - The "most prominent" publisher would usually be the imprint. May be a judgement call.
B - All significant publishers, including the imprint and parent companies.
C - Every publisher associated with a single issue

Do Whitman editions of DC/Gold Key books get special treatment and if so, what?
C - Include both the regular publisher and Whitman on the Whitman variants.

What about one-off joint editions like Jayco variants or Wizard 1/2 issues?
C - Include both the regular publisher and the joint publisher on the individual issues.

I'm golden with all these.