This has been asked in the past with regard to a muktzeh key, and i was uncertain if it would be the same with something like a usb. If i have a keychain with a usb on it that i wear week round, come shabbos is it ok to wear it and only use the housekey? The usb is one of the flat variety, unobtrusive and plain black (although i doubt it matters).
It seems that the USB should be a Kli Shemelachto Lissur, which would be forbidden to move unless you would be using it for a permisible purpose, or you need it's place (It may be also muktza machmas chisaron kis because people don't use usb key-chains for other purposes).
However, http://www.revach.net/halacha/tshuvos/Shevet-HaKehosi-Key-Rings-on-Shabbos/2185 says that the Shevet Hakehosi says that all keys on a keychain are a single unit, and one would be allowed to keep a muktza key on a keychain. Therefore, the law by a USB should be the same.
One of the ground rules of muktzeh is that if you have a container with both muktzeh and non-muktzeh items, the container itself is not muktzeh.
Some have the custom of lighting shabbat candles only on a table with other things on it (such as food or silverware) so that the table itself can be moved on shabbat if necessary. See this halacha yomit for more sources.