Which gears combinations shouldn't be used? Is there any general rule or recommendation to avoid usage of certain gears combinations (for 2xN and 3xN gears systems)? Do they differ for mtb and road bikes? 
I know that it's recommended not to use biggest front chainring with big chainrings on cassette (and opposite) because parts will wear faster and I will loose a bit of pedaling efficiency, but I'm not sure, if I should avoid 2 or 3, or even more biggest (smallest in opposite case) chainrings on cassette.
This is an old chestnut from the days of 5 speed freewheels and chainrings without shifting ramps. With modern hyperglide cogs and the relatively slinky thin modern chains, cross chaining is simply no longer an issue. While there are very few studies on this, the one I've seen suggests that there is no loss in mechanical efficiency for cross chaining at the angles typical of most bikes. 

In general for a given gear ratio, big/big is more mechanically efficient than 
small/small. So the only science out there suggests that cross chaining on the big
chainwheel is actually more efficient. 

http://www.jhu.edu/news_info/news/home99/aug99/bike.html

Use the gears you like, check your chain wear and replace your chain often and the expensive bits of your drive train will last a long time.