I like to use goombas in the 'gib model' attribute instead of wood or MREs or the like. Crates are ok if you're in a whorehouse, distribution center, supply depot...but they don't belong at the diner, or in the middle of the river, and what not. If you have a space ship, use ultra-modern storage conatiners, not HL crates in true willy nilly fascist.
If you find yourself in a situation where the use of a crate seems appropriate, make them look pretty. Add some hazmat labels, or make it look opened or broken, or something different than the original texture.
Personally, I put goombas as the gibs for the crates. This seems break up the tension, in an otherwise scary map. This one time, my friend Mark suggested I use some palm tree mdl instead of goombas. Needless to say, I was tempted to direct rage towards his general direction. Instead, I just pretended that he didn't really suggest it. After-all, there is no use in making a juhunga out of something, that is, unless a full juhunga is warranted.
Happy Mapping!