I've got a range of sites that have them either in the content or outside, say fixed position so that they are always visible.
I havent noticed a big difference between the two, but I would say that I am often quite suprised by how few people actually use them. Most SEO you speak to will emphasise how important they are, but if you ask an average user, eg my Mum, she wouldn't know what half of them are or how to use them.
Much of the decision about where they should go will often be led be the design. Thats generally my approach, if they fit in and look visible then they go in the content, but if not they end up on the side. I do quite like the sideways approach as they are very clear, you can use other things to make them more visible, on a recent site I used a small gif to draw attention: http://thedoubleglazingfund.co.uk/