Let's get this out of the way right now. PhD programs are nothing like college. PhD != college.
Why is it so different? The faculty and administrators of PhD programs have one goal: to place you as a tenure-track assistant professor at a peer institution. They do realize (especially in STEM) that some of their graduates will go into industry, but PhD programs grow their reputations with successful placements of their graduates. If you don't want to be a professor, that doesn't mean you shouldn't do a PhD. If your target job requires a PhD or you can't imagine doing anything else, then by all means do it, but do NOT do a PhD because you don't know what to do with your life. That's what law school is for.
Obviously, Papist, you want to do a PhD because you're interested (and educated) in a particular subject, about which you gained some insight with your junior and senior year electives. Remember the professors who taught those courses? Ask them for advice. They'll be able to point you in the right direction with respect to potential programs and advisors. Assuming you did well in their classes, you've started a dialogue that will facilitate better letters of recommendation for you.
Aside from the usual considerations of program reputation, graduate placement, and "Am I going to like living here for 5 years?" is the safety net problem. In most fields, you work under a professor, but what happens if you go to a department that only has one professor in that specialty and they leave? Try not to put yourself in that position.
That said, apply to every program you might attend if admitted. $1000 for a bunch of applications now is a drop in the bucket compared to the rest of your life.
And how are you going to finance all of this? The short answer is you don't. Your advisor/department pays for it. It's generally a bad idea to accept an offer from a program that won't fund you.
Let's say you get into Stanford, Harvard, MIT, etc. Which school do you choose? I can't answer that but you know who can? Students are those schools. You know how you find out? Go visit them. Programs generally have visitation weekends set up for admitted students. Absolutely take advantage of those opportunities. Talk with students. Talk with faculty and administration. Check out the city. You might be living there for 5+ years and working with those people for 5+ years, so choose wisely. Remember, grad students can be surprisingly candid and will probably give you the most honest critique of their programs. Also, no program can force you to make a decision before April 15th. Oh they'll try, but you have rights.I want to make this especially clear, Papist, the job market in many fields is terrible.
(Just don't be that idiot who amassed 300k in debt for a bachelor's degree
) In philosophy, which is an extreme case, it's not unusual for any given job opening to receive three hundred applications (and that's in a good economy). Most other fields aren't quite that bad, but if you want a job, you need to be prepared to take any job you can get, even if it's the last thing you'd ever want.
Ask me about handling recommendation letters if you need it. I know alot about this stuff because I have quite a number of familiy members and friends who all pursued master or doctorate degrees.