I've been asking myself the same question. I have a pretty low GPA compared to most other applicants (3.26 in physics) and a PGRE of 740 this year, which is much better than the 600 I got last year. Most of my research has been in cosmology, with no pubs yet. I'm applying in HEP theory also, with an emphasis on nonperturbative string theory (yep, really went off the deep end here).
I have a similar problem with tests, but my research adviser told me not to mention anything negative in my SOP. It's best, I suppose, to let your recommenders do all the explaining. By the way, how well known are your recommenders? If the people on the admissions boards have heard of them, it will help a lot.
I suggest that you try applying to a few other schools, just to be safe. If you're interested in string theory, Texas A&M is a good school to apply to. NYU is also good for string theory. I would suggest USC for string theory, but after reading Helio's comments about it, I'd recommend against it unless you have a good reason for them to take you and have extra cash lying around to spend on application fees.
If you're into hadronic physics and QCD, you should also look into schools that are good in nuclear physics, like Univ. of Washington, Michigan State, Indiana University, and Ohio State. I'm sure I've seen many more schools with strong faculty in hadronic physics.
I apologize if I can't be any more helpful. I suppose I'm posting here because I'd also like an answer to this question. Then again, I doubt if anyone really can unless they're on the admissions board, comparing your application with the multitudes of 4.0/990 applications they get.
Last edited by Juston
on Thu Dec 04, 2008 8:54 pm, edited 1 time in total.