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It's really too bad about your gpa, because from your GRE scores you're clearly an intelligent individual. Here is an email I wrote for another redditor a few weeks ago asking about applying to neuroscience grad school programs. He was specifically asking about what to do to get into a good neuro program coming from a psychology undergrad (you're going to be in a much better position with mol.bio.), so it might not all directly apply, but it's still a bunch of info on applying to grad school in general.

So basically there are going to be three or four major components that will influence your chances at getting into a good neurobiology program. First, let me explain that you will probably have a better shot at cognitive science programs because, as you will discover as you explore programs, cognitive science degrees tend to be offered by psychology departments; which your education is obviously more directly geared towards. As you start exploring neuro. programs I think you'll find that most are interdisciplinary, meaning that the faculty are comprised of professors from many different departments. However, many programs are still offered by a psychology department, biology department, or some other, specified home department. The ones offered by psychology departments are the ones you are most likely going to have the best shot getting into.

So a graduate school application consists of quite a few items, here are the major things school's are going to look at.

1. GPA. To get into a good program you're going to need a 3.7+, depending on the school you're coming from. The less prestigious your school, the higher that GPA needs to be.

2. GRE scores. You have to smash it, that's all there is to it. I don't know what year you are, but I would suggest start studying the summer of your junior year and take it once that summer so that you can take it again if you need to in the Fall. It really sucks, but the GRE tests specific skills and there are specific ways to study for it. Get a GRE study guide book, it should have statistics in it, too, offering estimates of what type of score you need to get. Realistically you probably need to score in the 70%ile of both math/verbal.

3. research experience. You need to get as much research experience as possible. I was really fortunate that I had quite a few neuroscience related labs at my school. I had been involved in 3 labs by the time I graduated and run my own experiment with a full APA write up. I should mention that it didn't get published, but that, of course, always looks great on a resume, if it's a possibility for you (don't worry if it's not though, that's uncommon). It doesn't matter SO much what sort of research you're doing (though the more cognitive/neuro related it is, the better), it matters that you're doing lots of research. They want to see that you're used to being in the lab. Also it's a great time to build a relationship with a professor which leads to me to my next point:

4. letters of recommendation. these are Hugely important. You absolutely must take the time to get to know 2 or 3 of your professors WELL, and it's important that they like you--a lot. They need to like you enough to speak on your behalf; and it's your responsibility to give them reasons to speak well so they're not BSing, because if they are, it will show.

5. You basically need to distinguish yourself in any way possible. Become a member of Psi Chi (I was my chapter's president), be a part of your school's Psychology club, join any honors societies you can, etc. etc. You've got to bolster up that resume.

6. If at all possible, get an internship or work related experience to the type of program you're looking at. I worked as an assistant for a neuropsychologist for a little over year. Even though neuropsych. is a clinical field and I wasn't planning on doing any of that sort of work, it was another great experience I could add to my resume.

Last, when you are applying to programs, you need to take special care in writing your "Statement of Purpose", which is basically just a letter explaining why you want to go to their school/major in your program of choice. If you are planning to go for the research oriented phd in cognitive/neuro, it's going to be very important to have picked out 2 or 3 specific researchers from their program, and match your interests to some of the things they're currently studying. They want to see that you're interested in what they're doing, so you can jump right on board. and for that matter, if you aren't interested in any of their research, you shouldn't be applying.

Also,

once you identify professors you want to work with, send them a very brief email (just a couple sentences), politely stating who you are, and inquiring as to whether they will be accepting research students in the following academic term. If they're not, DO NOT list them as someone you want to work with on your application. Also, this way they're already familiar with your name, which never hurts.

I hope this was helpful. Let me know if you have any more questions in general or about what I just said.

P.S. Plan on applying to ~6-8 schools, if you can afford it. Just for reference, I applied to 6 (MIT, Duke, UNC-Chapel Hill, UC-Boulder, Emory, and UGA). Chapel Hill is the only one I got into and that's where I'll be starting my phd in Neurobiology in a few weeks.

Why don't you try Europe? Germany has some excellent Neuroscience programs, especially in Berlin, Munich and Tübingen.

I studied for a year in Munich, a year in Berlin and now I'm doing my PhD at the MPI for Biological Cybernetics in Tübingen. They allow you to study at different Unis without paying fees everywhere. Lots of scholarships available. In Tübingen and Munich (2012/13 WS onwards), they'll award you 720 € per month scholarship even during your Master's phase if you're an international student.

I got to attend lectures from some of the world's leading scientists at the Max Planck Institutes, the Bernstein Centers for Computational Neuroscience and of course at the Universities. They're quite rigorous and thorough. In Berlin especially, most exams are oral conducted in the old German fashion. Quite cool. Some exams in Munich and Tübingen are also oral. In Munich, Berlin and Tübingen, you get to do 3 compulsory research projects in different labs and you can even get funding to go do one research project abroad. There are lots of hands-on practical block courses. The lectures can be pretty boring because of the difference in German and English rhetoric but you get by.

The programs are structured very loosely with very few compulsory courses. There are a wide array to choose from, unfortunately not as comprehensive as at US/UK Universities. But of course if you speak German, there selection might be wide.

Low cost of living for students, no fees (not in Berlin, Frankfurt and in NRW), and scholarships/stipends...its pretty nice. Even where you do pay fees, (Bavaria and BW), you end up paying less than 600 € per semester, that is less than 1200 € per semester and this includes fees and contributions to the Studentenwerk, from whom you'll get housing, discounts, social programs, subsidies cafeteria food, own libraries and semestertickets (for subsidised travel).

My lab does auditory neuroscience (mostly audio-visual multisensory stuff) and we're moving to Glasgow soon. If you need any more information, feel free to PM me.

Good luck.

Edit: Frankfurt is now expanding in a big way into graduate programs and its Neuroscience base. They got Erin Schumann and Gilles Laurent from Caltech and Ilke Diester from Stanford and a host of other people. Their program is new but it looks solid.

Edit 2 : Zürich and Lausanne have some of the world's largest concentration of leading neuroscience labs (Helmchen, Gerstner, Markram etc). And so does Amsterdam and Nijmegen with its Donders Institute. The University of Bologna recently started an interdisciplinary PhD programme in Neuroscience in collaboration with UCL London, INSERM France and others.

If you do your PhD in Europe, then you're assured of either a stipend or a proper salary with social benefits (more common). So there're no more loans to run up and you get time to properly do your research in peace :).

Edit 3: If you're interested in auditory Neuroscience, Munich, Amsterdam and Oxford have a lot going on in that.

If I were you, I would take a year or so more and get some stuff published, and that way you'll have a better chance at a really top school. I know some people at WashU are doing things you would probably be interested in, but your GPA might be a bit low for the school. I would also take a look at Northwestern, but the same qualifier applies.