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Originally Posted by Ninjinister
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Yeah, to extrapolate on this a little further the Batman crossovers were mainly produced by DC and BOOM is in charge of the MMPR crossover, so in a sense the Turtles are 'borrowed' characters for those series runs.
The X-files crossover was all IDW however, but doesn't count as canon as it simply doesn't fit
anywhere in the established continuity.
Other than that the only other oddities connected to the series are the Infestation 2-parter (canon), Deviations (not canon) and 20/20 (possibly canon).