I carry the PARK TOOLS "Super Patch" kit, aprox 1.5" square & thin plastic box. Self adhesive patches have worked for me mountain biking. I was wondering if you have considered having a spare tube with you? There are small triangular seat bags that could hold it and after a while, you'd hardly notice it on the bike.

I commute with a trunk bag, so I've always got a spare tube & patches. My mountain and road bikes have the little triangle shaped seat bags.