Speaking as one who has taken fish oil in generous amounts daily for 3 or 4 years, I've not seen any clinical downside to it yet. My fat profile shows a bit of omega-3 dominance, at least over what's considered "normal" but nothing in an extensive battery of lab tests show up any problem areas. And I seem to rarely catch a cold or flu anymore. (Paleo eating helps that, too)
I'm taking 1 to 2 ounces daily, right from the bottle (it's not as horrid as you might think). More than anything else I've done, this seems to be the one thing that has kept my meniere's symptoms from flaring up. I've gone at least 3 years without any major symptoms - which is practically a miracle in my book. I recently had a 3 week flare-up of symptoms but that seems to have abated (I upped my dose of fish oil for a few weeks, that may have helped resolve the flare-up - and also started taking fairly high doses of antioxidants).
Since the fish oil just keeps the meniere's at bay, not curing it, I assume it's the anti-inflammatory properties that are the main reason I'm seeing benefit from it. I had hoped the fish oil and phosphotidyl choline would help build better cell membranes which might fix the problem, but I wasn't that lucky.
As for Ray Peet, he surely puts out a huge amount of data to more or less support his point, but I think more evidence has been left out than included. From my readings on fish oil, it looks like his data is pretty much cherry picked to support his bias.
His article points out nice and clearly how finding truth amidst the vast quantity of research papers is surely a task needing ariadne's thread to follow. So much of research data now is bogus - as SOTT articles keep showing us.
What I'm seeing in his article is the use of micro-data points to support a macro position -- uhh, let me try to explain that. Some, or even all, of the research he relies upon may be accurate in a specific context, but in the big picture, ie the clinical effects on human health - it won't be relevant. For example, you can make a fuss over lipid oxidation, but oxidation is essential to continue living. If oxidation isn't balanced with antioxidants to keep the cycle of life going, then yeah, you develop problems - but oxidation isn't bad in and of itself.
OK, I didn't argue that too well, but hopefully you see what I mean. I've been trying to sort out truth from disinfo in the area of health and medicine for years and it's just astounding how how complex the disinfo is. It's no wonder Ray Peet might have misled himself, even if he had the best of intentions (which is questionable).
Based on what I've read, and what I've seen of Ray Peet's article, I don't see any reason not to supplement with a good quality fish oil. Be aware, though, that the BP Gulf oil spill chemicals will get right into the fats of any fish exposed to it - and I think that means many fish in the north atlantic. Also be aware that the radiation from fukushima (and elsewhere) is spreading rapidly through the north pacific ocean - I expect radiation to start showing up in this years salmon catch.