A year or so ago, I started to put museums in some saves, dedicated to storing all the collectibles and paintings my sims found/created. I've also included woodworking and other stuff they can put in their personal inventory. I made it a generic lot, so no other sim will go there. This is to NOT have huge, full basements. It can get a bit laggy, and of course add a lot to the weekly bills. I keep a collection, lets say crystals, until its complete. Then I move it to the museum for display. For displays, I use shelves on walls and dining tables, since they can hold a bit more than display tables.
If you are missing elements, don't sell duplicate crystals or metals. Send them off to the Geo council (vampires can crush them to get the elements, not sure if aliens also have such powers). Crystals can also be used with the helmet from Get Famous, and refined crystals can be used for powering jungle artifacts (its been a while, I forgot what they're called). So I always keep a few duplicates in a storage chest.