Many containers - wooden crates and metal boxes specifically - contain random loot which means that sometimes you'll find something in them, other times you won't... and perhaps you may find different items when trying at different difficulty levels, different savegames, etc. I haven't established a true understanding of how it works yet, except that for some of these containers it just seems random. What affects it I cannot say at this point. But... the crates and boxes included in this page have been confirmed to produce loot at some point, however whether they will for you (or not) I guess depends on "luck". Not all these containers provide random loot, their contents are fixed so that you'll find the same every time you play through the game.
The page covers items that can be found in each area, and each section has a map that indicates the individual locations; each batch of items has a unique number so they can be identified on the map and in the list below.
Thanks to everyone at the forums for the help in collecting information about the locations of many items included on this page. If you know of items that aren't inlcuded below, feel free to contact me; please include a thorough description of where you can find the items as well as a description of what the items include; if you could also include a screenshot and possibly a screenshot of the PDA map that would be quite useful as well.