Given lots of complaints over the years about Virenque, and the recent mention in another thread about Rasmussen sandbagging the first TT so that he could break away later to pile up KOM point, here is my alternative proposal.
Take all the climbs of Cat 2,1,HC, time each rider's ascent on that segment of the stage only. Calculate aggregate time or aggregate points until the end of the Tour.
Maybe not so original, I suspect. I like the points version better because there is a bit more strategy, with perhaps teams asking individual climbers to bust out on particular days to deny points to opponents (on days when their primary KOM rider is tired, say), much like a team might prevent another team from picking up sprint points.
Anyway, there it is.