Hi! You didn't mention whether you are planning to be an artisan or if you're just wondering which mats have the best resale value but I can answer your question generally at least.
As you said, the "dirty" items can always be sold, either by vending them yourself or selling them to someone else. If you plan to just sell them, keep them as dirty. Once you "clean" them, then you will have to try to sell them individually and some of them are not as valuable as others. Also, cleaned they take up a lot more space (there are 10 different rune stones and 10 different zodiac stones for example). Chemicals (like essence, elixir etc) can also always be sold. Be sure to check around for the best price each time because the shops and prices change constantly.
For the rest- first take a quick trip to see Kiroth. He is one of the three NPC's towards the back of Junon Polis (on the way to the lighthouse). Anything he sells in his shop is something you don't have to keep because an artisan can just go buy a stack from him when they need something. He sells up to quality 34 of wood, cloth, leather and metal and some other assorted things. Anything else can only be obtained from monster drops or disassembling equipment. I've got an artisan but I am also cheap... err... frugal... so I keep pretty much all of my drops. However a lot of arti's prefer to just disassemble when they need something. It's a personal choice.
There are a few drops that you can always either sell to an NPC or not bother picking up at all. Off the top of my head- those ancient coins (bronze, silver, and gold) and also rusty bell, colorful paper, match and ripped book. Those are not used for anything from what I've seen. I'm sure there are more that I just can't remember atm.
Anyway, don't know if this helps you or not but feel free to pm me here or whisper to me in game on HoneyBuns or Sulky if you have any questions and I'll be glad to try to help.