The main differences in fish oil are the levels and ratios of DHA and EPA, the type of fish used and the contaminants.
I'm not a huge cod liver fish oil person, because I'm not a big fan of high Retinol or Vitamin A levels or companies that put too much retinol back into the refined product, because this can interfere with the Vitamin D benefits.
I've said this time and time again, but I truly believe that Nordic Naturals, Carlson Labs and Metagenics (who all get there fish oil sources from the same distributor in Norway) have the best (lowest mercury, PCBs, lead, etc) fish oil of any company. Recently Barleans has started purchasing some of their fish oil from the Norway distributor as well... and you do get what you pay for!