I also had Thule racks for my old car (96 Olds Achieva):
177 fit kit, 400 feet, 50 bars
I did some thorough research and discovered Thule is test marketing a new rack for the Prius; however, I couldn't find anyone who could sell it to me, because it's apparently only available in limited locations and numbers. Here is the plan, if it survives the test market:
1103 fit kit, 750 feet, 762 bars
These bars will apparently be compatible with all Thule accessories, but I only have one accessory (load stops), and none of these parts are the same as the parts on my old Achieva, so I have no reason to stay with Thule. Note: these parts are all Prius-specific, so there is no reason to expect they will work for any future car you might buy.
So, I investigated Yakima. I found they advertise a set of their standard parts to work on a Prius:
Q towers with 48" bars and clips Q31 and Q32 (I think it was a pair of Q31s on the front bar and a pair of Q32s on the rear bar)
These are available now in stores and are standard parts, so they should be portable to any future vehicles. I'm not as happy with their equivalent of Thules's load stops (I use my rack primarily for transporting lumber and other building supplies home from the hardware store), because Yakima's are much shorter than Thule's, so I don't think they'll hold 2x10s very securely (for example). I may have to make some modifications...
I haven't bought Yakima yet, so I can't report on how well it works, but that's my current plan.
I also have a trunk-mounted bike rack that I used on my Achieva. It's a Rhode Gear Speedster Shuttle 3, and it fits well despite the Prius' spoiler and short trunk lid. The only potential problem is the lower bar sits right on the Prius' license plate, partially obscuring it. So far, I haven't been pulled over, but if a trooper or officer ever complains, my plan is to just unscrew the plate and put it in my back window for the rest of the trip! (I keep a screwdriver in the trunk with my other tools.) This rack is nice, because it is mounted entirely to the trunk lid, allowing you to open the trunk even with bike(s) (up to 3) attached, and it goes off and on very quickly and easily.
I've also heard of someone (I think it was http://www.john1701a.com
) who had a trailer hitch mounted to the metal rings (attached to the rear corners of the underbody) so he could use one of the post-mounted bike racks.
Note: when I took my Rhode Gear rack on the highway recently, I noticed a dramatic drop in fuel economy (6 or 7 mpg less than normal), and I suspect roof racks will cause similar drops, so whatever you choose, make sure you only carry it when you need it.