I found out a method how to identify them, but that requires UL expansion. If you let a sim with science skill "scan" (or analyze or how's the action called) the seed, and the action is successfull, you'll get a sample in your inventory. Sample of the plant's seed (it'll say something like "flame fruit seed" or "lime seed", not "unknown rare seed" sample). That way, you know what it is. But to know which seed is which with multiple seeds, you'll need to fin a way how to not mix seeds up - possibly having them in a chest, taking away one, analyze, plant if it's a seed you want or put in other chest if you don't want to plant it yet, and repeat.
On level 9+ you can even clone them. So if you're in need, make a few samples of moneytree seed, clone, enjoy!