Cardboard boxes. I never seem to have them on hand when I need to make something.
For example, Filbert is in my campsite, because I'm working on getting him back in. He wants a cardboard chair. It uses 1 box. Guess what I don't have? And the recycle bin is coming up bupkus today.
Normal wood and weeds. Also stone to a lesser degree.
I have about 12 stacks each of hardwood and soft wood, but less than two stacks of regular wood.
Weeds, I didn't realize how many of them I'd need to craft hedges (since hedges hadn't been released when I sold most of my weeds). Then it turns out I also need them for a bunch more recipes. The next thing you know, I'm down from three stacks of 99 to only 15 weeds left! But I refuse to use NMT just to go weed hunting, so I'm going to wait until a villager moves out so I can go island hopping and find weeds and a new villager at the same time.
Stone. I need so much. I foolishly sold it in the beginning not realizing how much I would need to use it.
I am okay with just about everything else. I have had to put all my projects on hold until I get more stone stacks since everything I want to make takes like a stack each.. why...*sobs in animalese*
Hardwood - I'm also landscaping so dug up all of my trees and replanted which means they're even more sparse haha. This is my third town and it's the first time I've had softwood and normal wood aplenty.
I don't usually go out of my way to build too many things...so I'm usually pretty good on materials for the handful of times I need them. I used to run out of iron when I first started playing...but I have plenty of that stored up at this point. I guess gold is an easy one to run out of...but, again...I don't really need that too often. And gold is certainly more of a luxury than a required material.