I sent this question along to Shawn Collins, who runs the splendid Affiliate Tips Blog and is, of course, the brains behind The Affiliate Summit conference that I regularly attend.

Here's what Shawn suggested:

There are two ways to go about running an affiliate program for your site: hosted on your server or an ASP.

As far as the hosted applications, I'd suggest looking into 1ShoppingCart.com and Groundbreak.com's Ultimate Affiliate Software. Both are attractively priced, reliable and robust enough for a basic affiliate program. The implementation for the installed affiliate software is more complex than an ASAP, but it's also more customizable.

On the other hand, affordable ASPs with a good reputation are AffiliateClicks.com, DirectTrack.com, FusionQuest.com and Shareasale.com. Implementation for any of these technologies is quick and easy - a matter of pasting some code on your purchase confirmation page. A little more than that, but not much.

You'll find that there are dozens, if not hundreds, of other options out there. I can't speak to the other solutions, as I don't have first hand knowledge of them, but I'd vouch for any of the above.

Thanks, Shawn. Personally I use 1shoppingcart for my own affiliate programs, through its rebranded front end of 1 Automation Wiz, which gives me good hands-on service and assistance too. It works very well for me...