Exercise for meditation sitting I couldn't find this exact question asked before. 

What kind of exercise is recommended for better physical comfort and "endurance"/"stamina" when sitting in meditation; apart from the sitting itself? 
I usually sit in the half vajra position, which is quite comfortable and stable, but find it a bit tiring when I sit for many hours. 

Any good exercises in "the long run"? Any good stretching or other exercises between sessions when sitting whole days?
The single best stretch you can do is the straddle stretch.  The linked video is pretty fantastic in that it not only shows you the ideal, but also the progression leading up to it.  Honorable mention goes to the frog pose.  I also really like this sequence from Kelly Starrett.  Ultimately, what you are going to want to pay attention to is hip mobility.  Most meditators experience pain in the knees and back and tend to focus on stretches and exercises that target those two areas.  Unbeknownst to them, what's really at issue is hip and psosas tightness.  The pain they experience is a symptom of a problem farther up along the movement chain; it's being caused by the body trying to adapt to a less than ideal condition imposed by poor mobility elsewhere.  Loosen up those other areas and the discomfort will lessen significantly. 

And for the record, meditating for long periods of time should make you tired.  That's kind of the point.  ;-)