I've spent quite a bit of time in purchasing my mountain bike. It started a year ago when I decided I wanted to be able to ride on more that just paved trails and roads with my road bike. So I started reading about mountain bikes and looked at Trek's line up because I already owned a Trek road bike that I'm very happy with. I read the differences between 26" and 29" bikes and understood the trade-offs. I was originally looking at purchasing a 29er Wahoo or Marlin. I wanted to be able to put 700c tires on and basically have a hybrid bike. I continued reading up on different components levels of quality and brand. I learned that despite liking the idea of 29" tires the frames were just too tall for me. I stand 5'6" tall with an inseam of about 28.5". So I decided that in order to have a "safe" stand over height I would need 26" tires. The next thing I looked at was top tube length. I stood over a few bikes and had space with 15" and 17" frames, but of course a 17" frame would be longer. So I measured the top tube of my road bike because I find it a comfortable length. It measured about 21" C-C. When I test rode a Marlin this year I had the experience of trying Sram x4 rapid fire shifters and I learned I didn't much care for them. Perhaps I've gotten so used to my Shimano Flight Deck brifters that I didn't like having to use my thumb for shifting up and down. When I test rode a Fuji Tahoe with Shimano Deore rapid fire shifters which are shifted with thumb and index finger. I liked that a lot more. The next biggest factor for choosing by bike was the suspension fork. Most of the entry level bikes have Suntour XC~ forks with 28mm or 30mm stanchions. I wanted to have 32mm stanchions and the Tahoe line up started with a RockShox XC32. The last decision I had to make was what color and it was the deciding factor between two levels of the same model.

So to summarize and recommend steps to picking a (mountain) bike, here's what I learned:
1) Get the proper frame size - check standover and top tube/reach while riding. Online size calculators can get you a good starting point for frame size but you'll have to test ride or look into specific geometries to narrow it to one.
2) Decide what kind of shifters you like and see if you have a preference, it's something you have to use from the day you take your bike home.
3) Is there a particular feature you want, either a fork spec or perhaps hydraulic brakes, and is it within your budget?
4) Pick the color you like most. Some models come in two color schemes and others don't. Is the cost difference with upgrading to a slightly better bike for a color you like more?

I hope my experience helps other in their search for new bikes.