What do you do if you have three applicants none of which are married, do you complete three separate 1003's or do you put 2 on one and the remaining borrower on a separate one?

Two on one and the third on a second one.

However you want to....unless you are selling to an investor and that investor has certain requirements, there are no governing regulations for specifics of 'applications'.

While i agree to an extent, (and this doesn't match the OP's THREE applicant scenario), i couldn't get behind a system of having unmarried joint applicants fill out separate applications while married applicants are instructed to fill out joint applications.