Another vote for refurbished.
I bought the 100-400 zoom in December from the Canon store. Perfect condition and had a manufacturing date code of March, 2011, so it was essentially new. I also bought a 430 EX refurbished through Adorama. It arrived in a "refurbished by Canon" box. Again, perfect condition. My understanding is that all refurbished from Adorama and B&H are refurbished by the manufacturer unless otherwise stated.
I do find the selections confusing and seemingly random. They don't seem to follow any logic than I can deduce.
For example: I have never seen a single G series on the site, some lenses that have been in production for years are never listed (such as the 200 f2.8 "L" prime, or the 400 f 5.6 "L" prime), sometimes new products show up quite quickly, other times they never seem to make the list (The 7D and the 100 "L" Macro both showed up less than a year after announcement, but I keep waiting for the 70-300 "L"), there seems to be no relationship between the popularity of the lens and the listing (the 50mm f1.8 is on the list, but so is the 14mm f2.8 "L").
I also wonder where they get some of these lenses. I can understand why popular lenses would show up, but again, I wonder how they happen to have some of these high-end "L" lenses consistently in stock. Are there that many people who buy the 14mm f2.8 "L" lens and then return it? It's all a mystery to me.