I think quilting is the messiest craft there is! So many supplies to keep track of... threads... scraps... you name it!
Using bins and containers for projects and supplies makes a big difference for me. It makes cleanup quicker which means that I am much more likely to use them (elaborate storage for me means I don't use it!). Drawers and using every inch of closet space helps me too. I find that when my surfaces get cluttered I avoid my room!