I have them - BAD - and I'm on Topamax too. I actually don't really have any side effects at all now that I've been on it a while. The worse thing I ever had was a little tingling in my hands... and I honestly didn't realize it was from the medicine!
It really has helped, but I also have another medicine they've combined with it for me, but I dont' take any narcotic type stuff that I know a lot of people have to take.
How bad are your side-effects compared to the headaches you were getting? For me, my headaches were about 4 - 6 a month. The Topamax helped a TON for a very long time (several years in fact). It's only recently we had to increase my dose again and eventually add the other medicine - but I have really bad allergies that make it bad too.
I hope it works for you - migraines are HORRIBLE!