Here's one assessment from a medical school website:
http://www.umm.edu/altmed/articles/flaxseed-oil-000304.htm
I read a while back that the omega-3s are bound up tighter in flax seed oil than they are in fish oil, so for someone with an inflamed gut and probably poor digestive processes, fish oil would be better.
For me personally, I take flax seed oil. There is less of a concern with mercury content, and I don't feel guilty about over fishing the menhadrin. Plus no fishy burps, LOL.