I use them near my depot settlements since these usually fill up and I find it weird to have units just kinda standing around the place.
I also like to put my police detachments in them when they are not rolling around the countryside chasing aphistamenoi.
If I am advancing into enemy lands as part of a major campaign I will also use forts to "stage up" my garrisons, so my main armies can keep on the offensive - although this sometimes does not work as the towns are too large to garrison easily and I am loathe to exterminate people and give my generals nightmares!
Hm, it seems like I use them a lot, but mostly I try to keep the ones I build rather than adding lots more of them.
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