I oftentimes fill out applications online unless the company requires me to submit the application in person. Are there any benefits to submitting an application in person rather than filling it out online and do companies sometimes give preference to those who apply in person?
I give preference to candidates who follow my instructions. If my instructions specify online submission anyone who walks in and hands me a paper resume is probably getting scratched off the list as "unable to follow simple instructions".
Absent specific instructions I'd say it depends on the job. If we're talking about a secretarial/reception position a candidate who comes in dressed professionally and conducts themselves in a manner I would want representing my company will probably have a positive note scribbled on their resume and maybe a leg-up in the hiring process.
If we're talking about a non customer-contact position (say a back-end software developer) where I'm going to be scrutinizing technical attributes of the resume a brief handshake and handoff probably won't make much of an impression on me either way, particularly as the interpersonal "team fit" part of the interview is something your peers would have to tell me about.
I would definitely consider your personality as an applicant in the decision: if you want to hand in a resume in person it helps if you're the kind of applicant who can converse for a minute or two with the person you hand your resume to (it may be just pleasantries and smalltalk, or not even that at a busy office, but if you're a "cold fish" it might negatively impact your chances).
Also consider the type of business: Selling something (cars, insurance, software, houses) is a very personal thing, and getting your face in front of the prospective employer can be a Good Thing.
It should go with out saying that you should have the appearance and demeanor appropriate to an interview. If you show up dressed well, conducting yourself professionally, and seem generally like the kind of person I'd want to work with I don't see a downside, and there's a chance it could help you out.