I've mainly used the leatherette box from PSI. I have, in the past, used the tubes as well. The tubes allowed me to put a card with a description of the wood (came out pretty cool). I saw someone (I think on Etsy) that sells them in a cardboard box with their logo and contact info on the top of the box. I would try that if I thought I could sell enough.
I would say it depends upon your price point. If you're selling 'basic' stoppers with chrome bottoms for 20 or 25$ the plastic tubes should suffice. If you're selling laminates, custom acrylics, or stone that garner $70+ I'd use a box... at that price point you should be able to fit the box cost into the price.
I don't put them in a box... I keep packages of white tissue paper and wrap everything I sell in the tissue paper after the sale.... I had some gift boxes for a while, but have run out of most of the sizes and haven't replaced them yet.