I have no experience with Nikon gear, so I refrain from doing straight comparison btw bodies, brands, etc.. but before you switch, do your math: selling a body & lenses, and buying new lenses & body will cost a bit and much more than just getting a new body... On top of that, if you're happy with your lens & flash, why switch?
To me, the Ltd are the reasons to move to Pentax, but that's a relatively expensive reason. For some others, it's Shake-Reduction & weather-sealing... See what is important to you... I see that the 16-50 & 50-135 are mentioned - they exist for Nikon, in a cheaper, not weather-sealed Tokina version... DA12-24 ditto...
To answer more directly what I can answer...
- K5 having cropped sensor as well? So, attaching 50mm lens to it will give me ~85mm zoom?
[Eljaco] Yes - but 50*1.5 = 75 angle of view, not 85
- RAW files (or however they called in Pentax world) - what software could be used to process/batch process them? I like Capture NX2, but that`s something for Nikon
[Eljaco] Personally i'll favor Lightroom 3, but they are cheaper alternatives: DxO 6.5, Bible Pro, Silypix, etc.. Just like for Nikon or Canon or Sony... in fact
- What Nikon camera is direct competitor to K5? I saw comparisons with d300s, d7000 and even really good and expensive d7000...
[Eljaco] To me the K5 sits in between D7000 & D300s... If you decide to keep Nikon, consider a D300, shouldn't be much different from a D300s IQ wise... & cheaper (compare the feature set, and see if the differences are important enough for you...).
- I have big hands - is k5 + grip is handy enough for people with sports background?
[Eljaco] We can't decide for you, so go and try it. The best camera is often the one you feel comfortable using and that you'll want to bring with you anywhere you go...
- Lenses - any good fast midrange, like Nikkor`s 17-55 2.8? What`s the story with lenses for k5 in general, compared to Nikon camp?
[Eljaco] I answered - on the new and still produced market, Nikon will have a larger range, but they will not the well-thought "crop" lens product range, and no limited. Ltd are the real Pentax deal.
In the range you mention, DA*16-50, Sigma 18-50 & Tamron 17-50 - from I read , I believe the Nikkor might be the best (as usual by a slight margin), but also the most expensive...
- "Stain problem" - should I worry about it?
[Eljaco] No. Worst case, you'll exchange your body, Pentax will cover that.
- Should I really consider k5 as an upgrade path from d80 (I don`t mind jumping the ship and sell mine Nikon gear at all)?
[Eljaco] It'll definetely be an upgrade, just like the D90, D7000, D300 or D300s...
I'd be you - i'll stay with Nikon. But then I'm a Pentax Ltd user, and I wouldn't switch the other way