Aligning pergola rafters to the sun?
A much simpler solution:
Build your pergola with rafters that are aligned in the most aesthetically pleasing manner to you (this is a personal preference and none of us can answer that for you). Then, once it's built, plant some leafy vines at the base of each post, or in pots near the top and train the vines to cover the roof.
As the vines grow, they'll produce leaves in the summer that will block the sun. During the winter, the leaves will drop off (providing you with some nice compost material), letting the sun through to warm the house.
Placing the rafters non-vertically will look odd, to say the least. Running the rafters at a not-parallel or not-perpendicular angle to the house will look odd.  After explaining it, your more environmentally conscientious friends may be impressed by your cleverness, but, when it comes time to sell, you probably won't be there to explain it to a perspective buyer and the weird look may well put them off before getting a chance to hear about your cleverness.
Additional considerations:

In order to allow the most sun through, you want the rafters aligned north-south and standing on edge. In order to allow the least sun through, you want the rafters aligned east-west and laid flat. You've got some diametrically opposed options there, and it's going to be really difficult to reconcile them.
The average winter highs in Denver (Dec-Feb) is in the mid 40s (F), so you're not likely going to be spending a lot of time outside. You may grill on the back patio (everyone likes a grilled steak no matter the time of year!), but that's one or two people outside for a limited amount of time - the sun factor probably isn't that significant.
If this is a free-standing structure not close enough to the house to notice a lack of symmetry to the house, do what you will with it! Letting the sun through to warm the house won't be a factor in this case.