Ahh! I feel so much for you right now. It seems like you're in the exact position I was in for so long and then I *finally* got a job offer last week. Maybe if I tell you what I did, that would help?
Unfortunately, I had applied to all the major chains, too, but I was getting nil response from anyone, either. I seriously don't know if it's just the market or no one looks at your online resume/application?
The only time I suspect applying online helped me was when I was contacted by a Target recruiter via email about a few positions and she said something along the lines that my "information was in the system" and if myself or anyone else would be interested in the position, to reply. So, I started emailing with her and she asked me for a phone interview. (It was a rough interview. Many questions and every pause felt long and awkward. Given the choice with in-person and phone interviews, always go with in-person! That's just my two cents!) I also showed up to all the local chain pharmacies and dropped off a cover letter tailored to them and a copy of my resume and asked them to give it to their DM. I can't say that helped much for me personally, either, but it might be something to try?
Another retail interview came when I called around to my local stores and found out that a grocery chain was hiring. The pharmacy manager gave me the hiring manager's name and number and it took some persistence to get in contact with him (for the first 3 - 4 times I called, he was either "busy" or "not in"), but when I finally did speak to him, he offered me an interview. I had applied online for the position, but I don't think I ever would have been contacted if I didn't call him. I then found out in the interview I was competing with at least one other person with 15 years+ experience, but, hey, I'm sure I learned something from that interview, even though it was disheartening I wasn't offered a position.
My next interview was at a hospital and it came through a recruiter who was local. It may have just been me, but I noticed a HUGE difference in dealing with a local recruiter versus those who are 10 states away. It only makes sense - someone local is probably going to have a better handle on what's going on and have more/better connections. He offered some really useful advice and gave me the inside scoop on what the employers were looking for. He was/is great. Unfortunately, I was runner-up in that interview and the hospital went with someone who had previous hospital experience. I was really crushed because I wanted the job so badly.
After that, I just started applying to any and everywhere because I knew soon I'd be competing with a whole new round of new grads (this was around the middle - end of January). I just went to indeed and simplyhired, typed in "pharmacist" and my state, then clicked "sort by date" and applied to EVERYTHING that had been recently posted. Even if it wasn't something that I thought sounded very great, or if it meant I'd have to relocate elsewhere in the state. I would get up early and do this every day and I tried always to apply to positions that had just been posted to get a good jump ahead of the competition. At this point I was panicking. I realized I was getting into a seriously dire situation because I had loans to pay on and the deferments were going to be up in a couple months!
Finally, finally, I received a call from a LTC pharmacy for an interview. Was that something I saw in my future? Possibly, but I didn't think I'd actually end up there. I had a little experience with LTC during one of my rotations and I really played that up in my interview, giving examples of how I intervened to improve the residents medication therapy and how I felt the position was very rewarding, which was how I truly felt - it just helps to say that out loud in the interview sometimes. I was much less nervous during this interview thanks to the previous ones, and after touring the pharmacy/speaking with the manager, I was VERY excited and I think that translated, because I was offered a job. Also during my interview, I made it abundantly aware that I was fine working ANY shift and that I was very flexible and would be happy with any hours I could get. I think that was also a real plus because my interviewer commented on how another candidate seemed very disinterested once they found out the schedule they'd be working.
The best advice I can give is just to apply any and everywhere and be open and flexible, even if you think maybe the job isn't something you initially saw yourself doing. I'm hoping all of this might help you out, or give you some hope. If I was able to find a job after a long, long search, I think you should be able to find one, also.
I really hope things work out for you!
EDIT: Sorry this was so long. I really started out just wanted to share in your frustrations about how you hardly ever hear back when you apply online to retail/chain pharmacies (especially Wags - I had trouble hearing from them since I was an intern!) then I thought maybe I could help by sharing my experiences. I just know how frustrating it can be to be searching and searching and searching and waiting to hear back and wanted to help if I could.
I graduated in May 2011 and I had just a bit of intern experience outside of my IPPE hours. I worked briefly at CVS (briefly being about 2 months. I generally didn't care for the people I was working with and I've never really enjoyed retail), then I stayed on for a little while after my last rotation (which was at an independent) to help out at my preceptor's request. 
