I've just been looking into this very thing. I have tried and tried to find anyone that will compare the various programmes available, but have failed miserably. Thus, I've depended on ratings and very tiny thoughts on the products available in order to attempt a choice.
And that choice definitely falls to either iSale or GarageSale.
One of the BEST things that GarageSale offers is the ability to automatically put pictures you use for your ebay sales into your web server. Another bonus is that GarageSale is able to show you what listing options will incur extra fees which is something that I don't think iSale does. GarageSale also allows for a better preview of what your auction will look like when it is on the ebay server.
However, the thing that iSale has going for it is the fact that the user interface is A LOT better than the GarageSale one. iSale just seems to feel more "mac"y. If looks are important for you and you don't mind spending a few extra pence for having ebay host your photos or have a .mac account to use, this seems more the app for you. Many people have complained that GarageSale is dubious for adding a text into your auction saying you used GarageSale to make the auction. This is easily removable in the preferences panel, but iSale doesn't have it to begin with.
Overall, they do a lot of the same things. It seems to me that the iSale programme supports after-auction aspects more than GarageSale does. iSale has a very cool feature now, in its latest 1.5 edition, which allows the auctioneer to gather the information of buyer in a completed auction with one button click. I have yet to try this feature, however.
Overall, after having had both programmes for many days, I've yet to be able to decide which one is best. They are by far the best out of any programmes available, but between the two it is too hard to make a definite recommendation. It would be best to try out each as they both offer demos that allow for you to post 3 auctions for free

They are the same price, so price should not be a factor in deciding. Individual needs vary and you may find that one fits what you require while the other doesn't.