Without a photo to see clearly, it's hard to say exactly what's happening but it sounds as though they might have rust, a fungal disease. Snapdragons are rather prone to it. Since they are considered annual or seasonal plants and very inexpensive, saving them in not really practical - once present, rust is very difficult to control. The recommendation is just to get rid of them and replant the area with something else.

It does look like rust. Is there a way to fix it?
Here's what they used to look like:
http://i142.photobucket.com/albums/r112/AustinFelciano/Snapdragons1.jpg

This is what they look like now:
http://i142.photobucket.com/albums/r112/AustinFelciano/Snapdragons2.jpg
And here's the rust:
http://i142.photobucket.com/albums/r112/AustinFelciano/Snapdragons.jpg

Although I think that they had this last year too if I'm not mistaken. This year seems worse

Yep, that's rust. Once it is present to the degree your plants display, it is not worth treating. The recommendation is to remove and destroy the plants. You can Google 'snapdragon rust' to get more information. Spores will over-winter on the soil so the disease can carry over from year to year. Spraying with a fungicide is only going to be effective before you see any symptoms.

Here is a link that might be useful: snapdragon rust

Aw :( That was helpful, I'm just sad that I'll have to remove them. They were one of my favorites.
The exciting part is that removing them opens a big space in my garden, so I guess I'll be shopping for plants soon :-)