I can commiserate, I'm in a similar situation. My first few years at my school are far less than exemplary, due to struggles with depression/alcoholism, and later mild addiction. I took a few years off, though, and had stellar performance after that, but my GPA at my current school (Emory) is still a 3.155 (I took some classes at Georgia State University during my hiatus and made a 4.0, so if I include those -- which I have been doing for most applications! -- it's still just a 3.28). I have found, however, that it can help to email some people at the programs to which you're applying and describe your situation. U. of Akron, for example, has a GPA requirement of 3.25. Before I factored in my GSU grades I didn't meet it, so I emailed the program coordinator and explained (some of) the situation, qualifying it with my most recent performance and other qualifications. She told me to still apply, as exceptions and wavers are made when other areas may compensate. And I don't think U. of Akron would be described as a low-tier program......
So long story short, don't be discouraged!