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You certainly can have this engineered and built for you. How much has to be done "from scratch" depends on what it is you want.
If you are a do-it-yourselfer (but it sounds like you are not) you might want to pick up a copy of Circuit Cellar magazine (or check out their website). There are plenty of ads for USB-key-related development kits and programmable devices. (And related articles.) One of these might be a good starting point for your project.
It might be a good idea to look through a few issues of Circuit Cellar anyway, as it will give you an idea of what is possible.
I wouldn't overlook the possibility that what you want already exists. There are all SORTS of interesting devices being built in USB form factor. For example, there is a USB-key temperature logger. Just put it in some place where you want to monitor the temperature. After a few minutes, hours, days, or weeks, retrieve it, plug it into your computer, and you can read-out the logged temperature record. Or, how about a USB-key GPS logger?
There are quite a few general-purpose USB-key devices that contain a small, low-power programmable microprocessor, which can be programmed to do "something" either when plugged in to a USB port, stand-alone, or both. These can be used as a base for many USB-key products without having to start from the ground up.