Yes, there is a difference.
I often wonder why cable manufacturers haven't devised an official industry standard means of differentiating between a speaker cable and a regular guitar cable. Most of the time, they look exactly the same, and only a trained eye can tell the difference (once you unscrew the plug.)
Therefore, it's no wonder that most people don't think there IS a difference between them and I see people using guitar cables to hook up their speakers all the time.
While you can get away with it sometimes, there are definitely drawbacks, and a very real risk that you could blow your amp, and possibly fry the speaker with it.
If speaker cable always used Speakon or some other unique plug system, there would be no question.
Anyway, here's my basic explanation of why you shouldn't mix the two types of cable.
Instrument cable is meant to carry low-voltage audio signals. It is shielded, with a single conductor. What the hell does that mean? Well, voltage, like the signal that's coming out of your guitar, is measured as the difference between "hot" and "ground." Shielding is when the hot conductor (or a circuit, in the case of your amp or a pedal, etc) is surrounded by (yet still insulated from) ground. This keeps out interference. In the case of instrument cable, there is a center conductor (which is a stranded wire, wrapped in a plastic coating to insulate it from the sheild) and a braided wire wrapped around that insulated center conductor. That's the sheild, and it's also "ground."
So if you understand a bit about electronics, you might see that the insulator between the conductor and the shield creates something of a capacitor. The entire cable becomes one long capacitor (and if you are familiar with how they can work in a circuit like your tone control in your guitar, you will understand that the longer the cable, the duller your tone.) It's not that big of a deal with instruments, and some don't mind the loss of top end... Boutique cables even claim to not have this loss, but that's another story.
Anyway, speaker cables are meant to carry higher voltages, like that which comes out of a 1200 watt power amp. The higher voltage just needs to get to the speaker, and quick. You might even notice that when you're really pushing the power through a speaker cable, it even gets hot. Typical speaker cable might look similar to guitar cable, but it is a two-conductor cable, with no shield. It's basically two of those center conductors of a guitar cable, wrapped in a plastic outer jacket. Sometimes, speaker cable can even be what is called "zip cord" which looks a lot like the wire that plugs your desk lamp into the wall.
So we've established that an instrument cable has a good deal of capacitance. We've established that speaker cable handles higher voltages and can sometimes get hot. If you subject a guitar cable to the same rigors that a speaker cable has to deal with, you are essentially strapping a capacitor across your amp's output, and possibly heating up the cable to the point where the center conductor might even create a short with the sheild, thus shorting the output of your amplifier and most likely blowing your output: a transistor, a tube, or worse, a transformer. I've even heard of speakers catching fire.
I can hear it now. "I've been using a guitar cable on my amp for years and nothing has happened." Sure. Even I've done it in a pinch, and you can get away with it. That said, you really shouldn't take the risk. If only cable and amplifier manufacturers could devise a standard (maybe 1/2" connectors instead of 1/4"? maybe Speakons? Maybe an XLR-style locking two conductor plug?) then there would be no danger of ever mixing the two.
I just feel that not everyone realizes that there is a difference. I don't even think a lot of people who sell you the stuff at the music store know the difference. If you know the facts, and then decide to take the risk, then it's your problem. Otherwise, I suggest putting a piece of colored tape or something on your speaker cables so you can tell the difference in a hurry.