In my campaign, I've usually gone with the "stake as a coup de grace" suggested above, but I've also allowed the following...
The stake always counts as an improvised weapon (-4 attack), provoking an Attack of Opportunity (regardless of any special combat feats the PC may possess), and it requires a confirmed critical hit to succeed. In other words, the player basically needs to roll a natural 20, with a confirmed threat at -4 attack, while copping an energy-draining AoO for their bravery/stupidity.
This is pretty desperate stuff at low/mid levels. Vampires have excellent dex and Combat Reflexes as a bonus feat, so even if the whole party is attempting to stake it, that's a lot of Attacks of Opportunity on them. Many more than if they just tried to engage the vampire in straight combat.
Of course, I'm sure there's ways to munch around this ad hoc rule, especially at higher levels... but it added a huge amount of tension and excitement in my experience, and was a little bit different from the usual "whack it 'til it runs out of HP" combat style.