I've noticed this on thefader.com. my concern is that this is a uncommon place for a subnav and will be mixed-in with ads. further, our site is pretty content-heavy. thoughts?
Left hand secondary or top secondary seems to be standard because of the order users scan a page (F-shape) but I have seen not much research to suggest right hand navigation is that much worse than left.
Navigation should be obvious and easily acquired by the user. Now, you alluded to the fact that your navigation is mixed in with adverts and the like; this might cause a degree of banner blindness and confuse the user and this is a problem. Position is not the main problem here, its the fact that you have mixed up other page elements with the navigation, and this, I think, is high risk.
summary **keep navigation elements consistent
**don't mix up with other page elements
Your concern is warranted. The right hand column is often filled with ads, so users have been trained to ignore the right hand column. This also agrees with the widely cited empirical data that shows that users typical scan a page in an 'F pattern.'
The following article by the Neilson Norman Group (a reputable authority on usability) gives some pointers on using the right hand column for navigation. If you're going to have navigation on the right, they suggest making it blazingly clear to the user that it is in fact navigation, by eliminating images, and of course any near by ads or anything that looks like ads, that would confirm or reinforce the bias already in the user's mind.