This is always a contoversial part of the game, as often time doesn't allow enough moves to make the decision beyond all doubt.
We often base victory on attaining particular objectives. This may be a particular position, preventing two enemy forces uniting etc. This still isn't always adequate as terrain may be held by units that are in pretty poor shape, while the enemy still has reserves etc.
Often it comes down to a gentlemans agreement as some aspects of victory are a little abstract.
For example, in my last game I lost a horse battery and an infantry brigade. The enemy had two routing units still on the board, and three units retreating. His heavy cavalry was severely damaged and retreating, whilst mine was fresh. His units had been separated by a river and all but two were able to unite with his main force (one unit on the wrong side was routing in the wrong direction). We both had reserves but I had effectively turned his flank and in subsequent moves would have been able to engage my oppenents centre from both the front and his right. He held a moderate sized BUA in the centre of his half of the table, some troops occupied this and some the open ground to its right.
Who won?
I don't know how you can factor reserves or a turned flank into victory points in any meaningful way other than an arbitrary value.
I have come across this method purely by chance and thought you may be interested.
http://www.miniatures.de/wargame-objectives.html
Ants