You could also include Ralts, Kirlia, Gardevoir, and Gallade.
I tend to think that what looks like clothes to us is just simply part of a Pokemon's skin. Humanshape Pokemon would just look odd without "something" to cover certain areas. Cases like Rhyperior, where an item is given to it, or Machoke, where its pokedex entry mentions the belt it wears to limit its power, are somewhat different though.
Not to sound macabre, but in Cubone's case, I always thought of it as wearing its mother's skull and using one of her bones as a weapon.
Burmy and Wormadam are one of the cases of Pokemon that wear "true" clothes, as the leaves, dirt, or trash cloaks are made from surrounding materials.