I really like to use oil based stains, especially on antiques. For one thing, oil based stains seem to cover better. For another thing, I think the beauty of an oil based stain is unbeatable. I believe that the more beautiful a finish I can create, the better it is for the environment. Whenever I refinish something for someone I strive for "heirloom" quality. I want it to the kind of treasured piece of furniture that they will keep for generations to come. If I can create an heirloom piece that will be treasured for another 50 years, I have done my job and helped save the planet at the same time. Think of the reduction in landfill waste if everyone's dining room table was so lovely that there was no reason to buy a new one, except every 50 years or so.
When I apply stain, I usually use a paper towel. Paper towels are cleaner than rags and they do not catch on edges as easily. I also do not have to deal with lint contamination when using a paper towel, and I use less stain too. I can usually get away with using only 1 paper towel to apply stain to an entire table top. Very little waste.
Make sure your wood is completely dry. The mineral spirits must be completely evaporated. Then dip that paper towel in the stain and get to wiping!