One of the advantages of the App Store model is that software is (AFAIK) easily redownloaded and reinstalled, so much so that I know people who have re-bought Aperture (for $80) on the App Store just for the convenience (plus then it can go on multiple Macs).
Why Rob Pike wouldn't fork over $80 for Aperture and save himself the hassle is beyond me. You can say "it's the principle of the thing; I've already paid for it!" but really? What is your time worth?
iWork can be had on the App Store too. Photoshop obviously can't but Photoshop should be recoverable somehow (right?).
These days I have a box with the few disks I need (Win7, MS Office), I store my personal files on Dropbox and any media gets stored on a hard disk. If my Macbook Air got stolen or just died I'd be up and running within 2 hours of getting a new one.
The only real annoyance for me is changing what computer your iDevices sync to. THAT is a major PITA. If you are migrating machines it's not so bad (but harder than it should be). But otherwise you need to backup, wipe it and reinstall everything and even then you lose all your iOS folders and so forth.
I don't like the iMacs because they're not built for replacing hard disks (amongst other things). The Mac Mini however is. If this had happened to me I would've been shelling out money to avoid the hassle and the whole thing would've been over in a day or two.
The moral I get from this post isn't how Apple is making things harder than they need to be (which they clearly are): it's that you shouldn't get caught up on the small shit that doesn't matter.