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Yes, there are differences in each service. What you need to do is speak with a healthcare recruiter to find out which service, (Army, AF, Navy) would be the best fit for you. Do not speak with the local enlisted recruiter since they will try to get you to enlist. Nurses (BSN) are commissioned officers. If you are a LPN then then you would go the enlisted route.
From what I've learned from talking to recruiters and other officers/enlisted people there are a few key differences. The pay and BAH is all the same in every branch. The sign on bonus can be different depending on the branch. The bases are different, from what I've been told the Airforce has the "nicest" bases. Although the Army seems to take pride that they dig in deep and forgo luxury to serve the Country, it just depends on your personality. Remember that the Navy is usually involved in coast or sea, and many people serve months on a ship with very little personal space. I've also been told that the Airforce usually is the best branch for continuing education.
Just some helpful hints from my own research, although doing your own research and talking with healthcare recruiters will give you the most information. Good Luck!