The primary application of atomic BEC systems is in basic research areas at the moment, and will probably remain so for the foreseeable future. You sometimes hear people talk about BEC as a tool for lithography, or things like that, but that’s not likely to be a real commercial application any time soon, because the throughput is just too low. Nobody has a method for generating BEC at the sort of rate you would need to make interesting devices in a reasonable amount of time. As a result, most BEC applications will be confined to the laboratory.
It’s not for lack of trying though. DARPA has a program aimed at applications of BECs to interferometry (Guided BEC Interferometry) which Chad mentions as one application. Research programs I mentioned some time ago are probably sill at it, though not all of them are intended to exist outside the lab.
Tch, tch – weaponize! An electron-positron BEC is a gamma ray laser at 511 keV, 9.00243 nm. Mirrors are left as an exercise for the alert reader. A superradiant gamma ray laser sounds a bit messy. Got Na-22?