Which camera do you prefer out of these 3 brands?

Canon, Nikon or Sony?

The question is on the title, and please give me reason why you chose the brand. I'm looking for a best- quality DSLR camera and it's affordable.

Sony is better, I'm a user, trust me

Canon

Nikon and Canon are the best of the three you've named. Personally, I chose Nikon because the Nikon mid-line and pro dslr's allow me to use virtually every Nikon mount lens made over severals decades (and I've got quite a few of those!) I love the feel, the operating system, and the results.

Sony has lots of bells and whistles, but I'm not a fan of any system that steals 30% of the light that passes through the lens (translucent mirror). The biggest deal-breaker might be this 2011 JD Powers Customer Satisfaction Survey. Check out the rankings.
http://www.jdpower.com/content/press-release/VSZkvvy/digital-single-lens-reflex-camera-online-buyer-study.htm

None. I prefer, trust and use only Pentax.

Sony DSLRs won't be around much longer as they are putting all of their effort into the NEX cameras.

Pentax probably won't be around much longer either as the brand bounces from one manufacturer to another.

Canon or Nikon (I prefer Nikon) are the only two long-term viable brands for a DSLR. Nikon just released two new high-end DSLRs this year, and are rumored to release 3 more.

It is likely all of the Nikon DSLRs - other than the D5100 will be new as of the end of the year.

This certainly raises the bar on the other manufacturers to keep up - even Canon.

Toss a coin. All are good. Nikon and Canon will let you take the system to the pro level. You won't go wrong with any of them. The camera does not matter much. At the same price point they are very similar. FOr in depth reviews, go to dpreview.com