I'm a fan of PHP redirects - cloaking - for a couple of reasons. First, it makes things way easier to manage on my end. If I need to swap out a final destination link, I can do it in my PHP file and not have to touch my individual pages. I also like that it makes my links look better to my visitors. If I were linking to eBay for example, the link would look like:
.com/visit?eBay
So, it's very clear to the visitor where s/he's going to end up. This also looks better to the average, non-techie visitor who has been trained by years of spam & scam scares to avoid clicking odd-looking links (I'm lookin' at you, CJ
).
I'm also concerned that Google may be demoting sites with affiliate links. I'm still reading up on that, but if it's true, this method could help with that.