I recently went through the same process - deciding between Nikon's D3100, D3200, D5100, and D90. Here's a quick snapshot of the advice I pulled together.
#1 thing is budget. Everything from lenses to software to basic gear, like a bag and memory stick, needs to be factored in. Figure out how much you have to spend first, that will make the rest of this process easier.
Physically hold the cameras in a store. This convinced me to NOT buy a Canon - I found the T3i to be awkward. I liked Sony and Pentax as well, though once I figured out what my budget would get me in terms of a camera and lens for those brands I realized my money wouldn't stretch far enough to get what I wanted. I liked the articulating screen on the D5100, and the pixel density blew the D3100 screen away. The D7000 - while out of my budget - was even more comfortable to me.
What are you looking to do with the camera? For me it's mainly taking pictures of my daughter around the house, as well as vacation photography. For you it could be the same, or it could be sports, scenery, portraits, wildlife, or a desire to get into doing photography professionally. You will want lenses for these specific scenarios.
Lenses are where the real $$ is spent. Depending on the model you go for, you might have kit lens options - see if that's the case. The kit lens will take good pictures, so don't think you have to immediately replace it. Going back to my situation - to take shots of my daughter around the house I'd want a fast prime, which would double as the perfect lens for night time photography. I'm a fan of zooms for daytime photography while on vacation, so that would be the second lens I would want to get.
How big are you into photography? What are the odds you will outgrow the camera you're buying? Two big things to consider. While you can typically return what you buy within 30 days, if you're going to put a lot of time and effort into getting really good as a photographer you might want to spend extra up front on a better camera. If it's a hobby that's fun, you might be best off buying the least expensive camera - after all, a DSLR is a step up from the vast majority of digital cameras out there. Don't get caught up in everyone talking about buying bigger and better cameras when simply buying a DSLR is already buying a bigger and better camera for you.
You may also find that the lenses you want do not auto-focus with anything less than a D90/D7000, or ones that would auto-focus with a D3x00/D5x00 are significantly more expensive, and it would be less expensive to pay more for a D90 or D7000. This probably will not be the scenario, but it's possible.
It spent a ton of time researching my options before making a decision, and if I had simply followed this advice step-by-step I would have made my decision much quicker.
Nikkor 18-55mm VR, 55-200mm VR, 35mm f/1.8
iPhone 5 for snapshots