I'm not sure I have much advice to offer, but I totally sympathize! I can at least offer my experience from both sides...
I have been with my bf for many years and several years of our relationship now have been long distance (not all at once.. it has been off and on long distance). I am finishing up my masters now and we are long distance, just a few states apart. The PhD programs I am applying to are on opposite sides of the country and I just don't think I can keep doing the long distance. As I said, we've done it before and it was great, but to make it work, you totally have to be committed. I'm just totally focused on other things now and not being the gf I should be. I can only imagine it will be worse once I start the PhD. The point of this rant? He is totally committed to making it work.. meanwhile as my acceptances from the other side of the country come in.. all I think about is that I know it is coming to an end... so I totally can sympathize! it's rough- he is a GREAT guy and I too have in the back of my mind that I"m being stupid and will end up a lonely PhD (but.. come on.. you can't think that way!)
From the other side of the coin- several years back my bf started working for a company and they gave him a choice of taking a position in the same location we were currently living, or overseas . We were in love and he chose to stay in the states rather than taking the overseas post (that he really, really wanted to take). I never asked him to stay, he wanted to do it for "us".. but I was thrilled he chose to. Well years later, here we are, and even though it was his choice, I feel guilty he didn't take that offer. He's never thrown that in my face, and it was his choice... but man, it would have been such a great experience for him. At that time, neither one of us thought we would ever break up.
So I think.. you just gotta do what is right for you, whichever decision that happens to be. I've done the long distance, I've done the "stay for the SO" gig, and I'm about to do the "break up due to distance" thing.. all with the same guy. They've all had their uncertainties and unknowns- you just never know how it will play out. But no matter what, things always work out in the end. So whatever you chose, keep your head up and good luck!