I had to make that decision a few months back when I had to move much of my stuff into a storage unit as I'm planning on house shopping next summer and my current storage options weren't cutting it. I don't have a lot of high-end stuff as I run postwar and traditional sized stuff. I keep all postwar boxes as after selling a F3 New Haven AA with the master carton for $4500 (for someone else unfortunately) I cannot bring myself to toss a postwar box. However most of the postwar I buy comes without boxes as I like to by lots offline, fix it all up, keep what I want, and sell the rest. So all in all, I probably have only two rubbermaid bins worth of postwar with boxes.
For the modern stuff I have I usually keep the boxes for engines and any car that has detail parts like flatcars with stakes, etc. Williams boxes I find to be way oversized (and most of the ones I had the glue had dried out), so I ended up getting rid of a bunch I had for standard 15" aluminum passenger cars. Those reduced storage space by about half for those cars. Accessory boxes, especially for some of the MTH remakes I have of small postwar stuff like crossing signals are way oversized. I'm mostly an operator over a collector, so when I decide to sell something I can usually say I got most of my original purchase price worth in enjoyment of using it and I just shoot for whatever that item is going for at the time regardless of what I paid for it.
A related story, a year or so ago I bought a collection off a lodge brother who was moving out of state for work. The deal was I would take the collection home, evaluate everything, then give him 50% of the value so if I sold it I could make a little and if I wanted to keep some stuff it would be worth my time. Everything was in various cardboard boxes (paper boxes, gift boxes, appliance boxes) so I had trouble fitting everything in my suv, I even had stuff in the front seat and some stuff on the passenger side dash. His family was helping bring stuff out of the basement and we were in a bit of a rush to load the car so everything was just going in without checking what it was. Anyway, when I got home I realized about two thirds of the boxes were trains, and the rest were boxes of empty boxes... The boxes all matched up with stuff that was there, and since we hadn't agreed on a price yet it wasn't like I got cheated or anything, so mostly we just laughed about how much we had to jam stuff in the car when it could have been much easier. Some stuff though was completely unnecessary like modern era lionel boxes for switches, but half were ripped and none had the inserts, so those made no sense to me to keep.
