On (working) military bases, and some industrial sites, you will still see plenty of crates (often reusable), pallets with built-up storage things for liquids or special purpose parts, and 10', 20', and 40' containers. Plus, barrels. I was surprised just how much bases in Iraq and Afghanistan looked like video game levels.
I was going to add how I thought Half-Life given its military bases is probably the only major shooter of its era that actually had a reason for all the crates and barrels. I think the circus you end up in (if I'm remembering the original game and not an expansion or total conversion) is actually the only other place I saw a genuine crate. Incidentally it was filled with food for the animals and not headcrabs.
My problem with most shooters is that the crates are placed randomly. At least in Half-Life the crates were more often than not in a storage room/area/rack than piled in the middle of a room or in an obscure corridor.
Fallout 3 resolved the box problem too, in that most items were actually found on shelves. Something I hadn't seen since the days of isometric RPG's where tables actually found their heyday.
