I love printing out papers to read. Being able to write notes on the paper is a huge benefit. In theory you should be able to do that on the computer, but even if that software was decent and ubiquitous and uniform, it still wouldn't be the same because writing by hand where you can make arrows and underline and circle things is so superior.
Something huge that's missing is you can keep important things open, or queued. You can put a post-it on a page and have that tab hanging out. You can put that paper on top of the pile so you see it in the corner of your eye all the time. That's of huge value - it reminds you to come back to it, it keeps it in your brain, you don't lose it in the mess of your computer. It can be spread out on a tricky page in the corner of your desk for weeks where you keep scanning it occasionally. You can keep stacks of papers to read together and on top of your pile.
You can also collate and bundle different types of data. Like some paper, some other paper, some pages of my own notes, paperclipped together. It forms a bundle of data and action items that is useful.
One of the key things is that these bundles are dynamic. We see that perhaps even more so with CDs. Yeah you have your filing, which is alphabetic or whatever, but you form little temporary bundles. There's the pile next your CD player, which is partly a history but also maybe stuff you took out to listen to and didn't play. Then maybe there are piles scattered around, a cluster of jazz you took out cuz you wanted that one night, or a cluster of your favorite stuff.
These are all things we'd like on the computer.