Here are several:
1. What other sites did you develop? Ask for domains and the actual parts he/she worked on (i.e. design only, functionality of X, Y or Z)
2. What's your background? You're looking for someone with real experience, not someone with just a degree. You're also trying to figure out if he/she "thinks" on your level, because if they don't, you might not get what you want.
3. What other tools have you worked with? A good developer will have experience outside of a particular shopping cart - even if he only works with one cart. Those other tools would be MySQL, WordPress and the likes. This lets you know he can INTEGRATE things, rather than just build on a template.
4. Ask him if he's worked with any other professional people in related fields. For example, if you are also hiring an SEO strategist, he needs to be able to incorporate tags and such. If you're hiring a graphic designer, he needs to be able to incorporate those components.
These, of course, are just a few questions. The type of project and preferred language will call for many more.
I've been doing web development for about 15 years now and have seen some great methods for finding the right candidate. One of my favourites for finding a solid programmer goes like this:
Start by asking three questions. One simple, one medium difficulty, and one impossible question. The idea is to see how they think. If you can get them to work it out in front of you this is a great way to see how they will problem solve issues. The first two they should be able to answer, and the last they should be able to figure out they don't have enough details to do, and why. If they can't figure out that it's impossible, you can always let them know, but see if they can figure out why.
If you have to code in a specific language, ask questions about that specific language. Keep them relevant to your project. Same with if you're going to use some pre-made CMS, or what company you are planning on going with for payment processing. Find out if they have experience working with those things. This isn't always important, but can speed up the process. More important if your project is time sensitive. If they suggest using something else, find out why.
All of these things should make someone stand out for you. Sometimes it just comes down to a gut feeling.