Hi Pete
I wouldn't recommend them with or without an affiliate link if I didn't like them.
I personally use IDevAffiliate on one site and 1ShoppingCart on another.
1ShoppingCart is pretty much industry standard. It has it's ups and downs but is generally recognised as the best "all in" option for autoresponder plus shopping cart plus affiliate.
IDevAffiliate has absolutely superb reporting. From an affiliate point of view, I love it. I get stats that I can look at, with lifetime and drill down options. From a site point of view, I can offer affiliates this plus links that point to exact pages, integration with various carts & payment methods and enough different ways to track the sale that both myself and my affiliates can be sure that the commission gets to the right place. It isn't often recommended as it doesn't pay much (20% from memory).There's also the option to auto or manually approve new affiliates, set up a minimum payment amount, mass pay with Paypal, add a bonus for signing up, pay per click or per sale.
(Same as on outsourcing I'd always recommend Rentacoder over Elance but you'll rarely see that done as Elance pays out better...)
Affiliate Window I use from the affiliate side. They're similar to Clickbank in that you need to join each merchant individually. The merchant can set affiliates up to be auto or manually approved, can set restrictions on affiliates (but I suggest staying away from that as the more restrictions you apply, the less people will be inclined to promote - I just dropped a magazine program that was working OK and getting signups because they changed their terms so I couldn't mention the magazine name in PPC ads. Duh). There's also many different options e.g. text, banner, data feed which are more easily accessible than CJ.
Trevor
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