They may keep your resume on file, yes. However, in this economy, with new postings many companies and agencies are receiving so many resumes that they have no need to go to "the file." There is such a glut of resumes with any new posting that to add old, filed resumes on top would be administratively unfeasible.

I'm not even in HR, but when I've been a hiring manager, I've definitely kept resumes on file and given them a second look if something suitable came up. Then again, I've also strong-armed HR people into handing over a stack of unfiled resumes when I really needed to start interviewing and they "didn't have the time" to go through the pile to find the resumes for my department.

It all depends on the company/quality of the recruiting department. in a perfect world, recruiters would use the ATS/CRM systems that collect the resumes to mine for potential candidates.
I would say the bigger, publicly traded companies probably do a better job of this than others.

Often, when I apply for a job, the automatic confirmation will tell me that the company will keep my resume on file for consideration for future/ additional openings.

Do you really do this? Look through applicants for other positions when you have a new position open up?

I'm mostly just curious, but also, I see that some companies to whom I've submitted applications then post other openings which are also a potential fit for my skills. Obviously, I would re-apply or somehow update my information if it was really a great match, but I'm just wondering how common the practice of looking back at previous applicants is. It's a very common claim on the part of companies.