1. When flying to airport that does not have ATIS, how to determine which runway will be in use for landing? Or this is normal to reach your last way point and only then receive clearance from ATC for runway? If it's so, then making a flight plan for specific running can be 50/50 gambling. Not a big problem with single runway airport, but would be nice to know in advance.
Even when flying to an airport that does have ATIS it has a maximum distance over which you could expect to receive it. I haven't double checked, so don't quote me, but I think it's about 80 miles in FS. Anyway, the best thing to use is PF3's ACARS system (default hotkey is #2). One thing you have to bear in mind though. with regard to determining the runway at your destination, is that nothing is 100% guaranteed... just like in the real world!
Firstly, PF3 determines which runway to use by checking to see if any AI Traffic is arriving departing and if so use the same runway. If there's no AI traffic detected, and there won't be if the airport is more than approximately 80 miles away (or thereabouts) because AI traffic is only active within that radius of your aircraft, it will use wind direction to determine which runway to use. Depending on which weather engine you're using and how you have it setup, this could change dramatically at you destination airport whilst enroute, so it is best to keep checking ACARS. (see the User Guide for more details on ACARS)
2. Arlanda case - anyone has any clue what happened? Is this normal to get info from ATIS for one runway, but be cleared for another? If I made a flight plan for 26 in a multiple runway airport, should I be expecting for this runway anyway? Other aircrafts were also landing on this runway. Was ATIS a fake message or PF3 mistake?
Please see my previous answer
3. And last one for traffic on the same flight. As I mention i nearly had a smooth landing in Arlanda. On final when about 4 miles to the runway, another aircraft taxi o the runway for take off. Well, it was still 4 miles distance, normal even in real world as long as I know. Soon it started to accelerate and took off. Good I thought, now I can definitely land. But just on the short final, maybe less then a mile, another aircraft taxi in to position for take off. Need to say, I did a crime, flew over it and landed anyway. I just did not had time to practise go around! So what happened here? Does PF3 not control other aircrafts, especially for take offs and landings? And I was not instructed by ATC to go around, so I guess it was thinking everything is ok.
PF3 cannot control AI traffic and only FS does that. Having said that we can and should stop runway incursions, in the same way as we stop other aircraft getting in your way during taxi to/from the runway. Always a very difficult issue to try and trace though if you have experienced problems but without a debug log we have no chance whatsoever.
Please always include the debug_monitor.log file from your PF3 ...\Logs folder by zipping and attaching it to your post. You could do so now if you haven't done another flight since this problem occurred. If you only done one more flight since it happened then please include the Old_Debug_Monito.log, but if you've done more than two more flights the evidence is gone I'm afraid.
It would also help when reporting problems to tell us which FS you are using