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This question answers whether a prior patent application can be used against a newer commonly owned patent application, but my question is what situations (if any) exist where a prior publication, or patent, cannot be used as prior art against a pending application?

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Assignee status itself has no bearing on whether something qualifies as prior art. In fact, if you look at § 102, you'll see that the only time who was the author of the prior art matters is for § 102(a), "the invention was known or used by others in this country..." For a published application or patent, the identity of the inventor or assignee does not affect whether it can be used as prior art against some other patent application.

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I should add that assignee status does affect what happens under double patenting, but that's a little different than prior art. – m3lvn Oct 30 '12 at 17:26
This is a technical answer: T is correct here to an extent. If the reference-in-question qualifies as prior art under Section 102(b) (statutory bar) then assignee status does not matter. However, assignee status does matter if the prior art only qualifies under Section 102(a), (e), (f), or (g). – Dennis Crouch Oct 30 '12 at 19:39
@DennisCrouch can you expand a little on the situations where assignee status does matter? – ihtkwot Oct 31 '12 at 22:27

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