Homomorphism and Zero Knowledge in FIPS 140-2 compliant systems I am analyzing a system that needs to be at least level 3 FIPS 140-2 compliant. The system may leverage from homomorphic and Zero Knowledge constructs, but, as far as I can see, the algorithms approved for FIPS are the most standard ones: RSA, AES, SHA-*, etc.

Is there a similar standard (or an extension to FIPS 140-2) that enables the use of (say) Lifted ElGamal or Paillier? If not, how could one evaluate commercial solutions that support said algorithms?
I'm no FIPS expert but I strongly suspect the answer is no. FIPS is incredibly restrictive and laughably behind the times. 

To evaluate those algorithms that don't appear in FIPS, first make sure their component parts are secure (maybe even built with FIPS algorithms as subroutines). Then, if there are known answer tests anywhere, maybe from the authors of the algorithm, you can test the implementation against those. Do a thorough code audit, making especially sure that the malleability of a partially-homomorphic scheme does not lead to a side channel somehow.

If you get to this point, the schemes will be better-audited than 99% of crypto code, and you can probably sleep soundly knowing that you did the best you could with a non-standard algorithm.

As an aside, exactly what "homomorphic" and "zero-knowledge" techniques does it use? The term "zero-knowledge" especially is thrown around a lot in industry, so there's really no telling what they're doing without more info.