Along with that question.... Who knows of the cheapeast place to get CF cards of 1GB or larger? I believe the Lexar 1GB cards are now $239 - $40 = $199 in many places. Is there a reason the price has dropped?
Compact Flash cards are much, much, much, much more durable than microdrives. Access times will be marginally faster since they are solid state devices while a microdrive is a spinning hard drive with mechanical latencies to consider. For the same reason, a CF card requires less power to operate so it will create less drain on your batteries.
The advantages of a microdrive used to be that they came in bigger sizes (not so true anymore with CF cards gettting up into multiple gigabytes these days) and that they were cheaper per megabyte than CF cards (but CF cards have been dropping radically in price as well making the differences neglibible when factoring in CF advantages).
As to why they prices for CF have been falling so much, all things digital fall in price, but one of the main factors in this case would be digital cameras. CF cards are now manufactured in much larger quantities than they once were, and the economies of scale in manufacturing benefits the consumer.
I would go with Compact flash way before Microdrives. Why? CF is much more durable, uses less camera power to write to and (At least with the one I used) have less of a chance of getting card errors due to file fragments.
I have the same issue in mind. Here they are doing a promotion on the 1G Microdrive. Its at the same price as a 512M Sandisk Ultra II. The thing I am concerned about is their relative durability. Does anyone know if there is any quantifiable information available?