In addition to Species 8472, I would say a number of Non-Humanoid species would be incompatible with the assimilation process as they do not have the same kind of brains and central nervous system as Humanoids:
1. Changelings 2. Horta 3. Tholians 4. Caretaker species 5. Insectoid and Aquatic Xindi
Although the borg can't assimilate the doctor's hologram, his computer is still vulnerable. even the Voyager doctor was at risk with his portable emitter.
Re: Species the Borg probably can't assimilate image for user timmytony80 by timmytony80 ยป Sat Nov 19 2016 10:38:50 IMDb member since June 2008 mariakelley04164; Seems 2 me it c/d just as easily go the other way. Sort of a Dyalecks vs. Cybermen scenario
Daleks*
BTW The Borg are pretty much expy's of the cybermen.
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I don't see why they couldn't assimilate any Xindi species - but Xindi aquatics and insectoids would be impractical given the norm seems to be to use humanoids on their ships - but then again, they did try to assimilate Species 8472, which is not humanoid. So it seems as if almost anything is up for grabs. They could potentially try to assimilate the Founders or any other "impractical to put on a Borg cube" species just to gain their knowledge, but not necessarily to make them drones.
If they Borg thought earth worms, kangaroos, whales, or Teletubbies had something to offer them, they'd go for it to at least gain the knowledge of the species, even if they'd be impractical to put to work.
Given that, I think it mostly boils down to species which are immune to nanoprobes, like Species 8472. And potentially "god-like" creatures like Q and the "Greek Gods" of TOS (but would they be susceptible if in humanoid form?). Same goes for non-corporeal species .
gambitcolumbus; Species 8467 used 2 be Borg-Proof! Until Voyager's Doctor vastly improved Borg nanoprobes. Apollo c/dn't handle the old Enterprise! Let alone The Borg!