Here's a list of some items that should be looked at for increasing the price. I will edit this with more if people give me more ideas.

-PEN Deboreka Necklace and Belt

-Garmoth's Heart

-Resplendent Alchemy Stones

-Splendid Alchemy Stones
-Shining Alchemy Stones as well (they rarely will sell, but might as well do this since it's worth a fortune)

-PEN Geranoa Accessories (this was a massive oversight by PA when raising the price of PEN Manos Accessories)

-Spirit Perfume Elixirs (Almost all of the perfumes as well seem to be sold out regularly other than swiftness and courage)
Spirit Perfumes entail: Dead Tree Essence. Loopy Tree Sap, and Fruit of Nature. Increasing the price on these could help, or increasing how much is obtained in-game. This could work with all of the ingredients for the other perfumes/elixirs. 

-All of the Cups for accessories (other than Cup of Arid Moonlight)

Would love to see if anyone else had any ideas of other items that are undervalued

Reason spirit perfumes are sold out isn't a price issue. It's because fruit of nature are hard to get. You can't really gather for them. Hoe gathering is how you get them but you only get like 50 per hour at 2k mastery (that number might be wrong, been a while since I last did hoe gathering). Even if you raise spirit perfumes price to 3 million each, it won't increase the amount of spirit perfumes made cause people can't really gather for fruit of nature. It's simply just a material bottle neck. 

On the other hand a whole bunch of alchemy materials and elixirs need a massive price increase. There are lots of elixirs which are price capped but you still lose money making them.