If your friend is a runner, honestly doing 3 miles is nothing. My mom does 3 miles for fun :) for her, anything over 5 mi is "training" - anything under 5 mi she doesn't even count. So, I would say put it into perspective when choosing a thank you gift.
I don't run nearly as much as my mom and I personally have too much running junk around my house. I know my mom has WAY more than I do, so I don't think I would give anything in the running department. Personally? I'd give a gift certificate to a local coffee or sandwich shop and call it a day.
One other thing - some registration fees for races are expensive. Sure, you get a t-shirt or water bottle, but it doesn't offset the cost of the registration. 5ks are usually pretty cheap, but some have music or something after and they use the proceeds from the race to offset the other costs. Perhaps offer to pay the registration fee if you haven't already. My mom and I specifically choose races that have lower registration fees - if you are doing a race or two a month, it adds up quickly!