I agree with your approach, getting the power out of the case is a great way to avoid cooling concerns.
When I first looked at the B3, what I wanted was a 240GB SSD but that is not an option. I considered buying one anyway and using the HDD somewhere else. The SSD I was considering (and still am) is the Corsair Force CSSD-F240GB2-BRKT-A 2.5" 240GB SATA II, 2W max, 0.5W standby (Newegg part: N82E16820233169 $309.99 + $7.56 ship = $317.55). With this SSD I would have a total maximum of 4W (2W CPU + 2W SSD but typically 2.5W) which would be low enough to satisfy me without air cooling. I have used this SSD before on Ubuntu systems and have had no problems. Also, reviews I have read on this SSD did not indicate user problems. The SSD comes with a 2.5” to 3.5” mounting bracket so it would be easy to install on the existing B3 HDD mounting rails.
Another alternative I considered (my second choice) was to order the B3 with the 40GB SSD option and equip an external HDD with eSATA to the B3. I have disks and cases that I could use so the cost would be zero for me. The case I like is Rosewill RX-358 V2 BLK (Black) 3.5" SATA to USB & eSATA Ext. Enclosure w/Int.80mm fan, Newegg part: N82E16817173042 $24.99. I really like this case and the fan is not loud. This alternative would also be about 4W inside the B3 case, but would have the cost of an HDD and external case if you did not have those on-hand.
I also considered the USB flash drive approach. You can get 32GB or 64GB USB flash drives for $40 to $100. This approach also runs into the problem of having to order the B3 with some storage. The most obvious would be to order the B3 with some HDD option and use this HDD in an external eSATA drive case with the USB flash drive as your OS drive. Now you have the added costs of just the flash drive and the eSATA case (about $75 to $125). This alternative would be just 2W inside the B3 case. With your approach of an internal HDD and reduced HDD usage you could get down to 4W (4W to 8W WD Caviar Green specification) for a total of 6W inside the case. As you point out, the USB flash speed and read/write lifetime must be a concern and I am uncertain what adjustments would need to be made, so I resisted this approach. Your suggestion of a tmpfs for /var/log and /tmp are undoubtedly sound, however there is only 512MB of CPU memory and I am still uncertain about other possible needs to accommodate the flash drive in this role. I simply do not have the knowledge and did not want to spend the time experimenting. I am very interested in hearing if you or anyone have more information on the possibility of using a flash disk for Linux OS operation. Doing a quick google search I came up with a few hits that lead me to suspect that this may not be easy and may require more memory than 512MB. See: http://www.cyrius.com/debian/nslu2/linux-on-flash.html
My final choice was to air cool the B3 with an internal air flow. This provided me with the maximum cooling under any configuration and allowed complete flexibility for any use or changes I might want to make in the future satisfying my “put it in and forget it” desire while allowing for flexibility. This approach had no cost for me but would be low cost if you did not have the parts on-hand. The down side is that you must build and modify, and you must give up the aesthetic appeal of the small neat package of a stock B3. To avoid these down-sides but still provide extended life, I would suggest that most users choose the B3 with a 40GB SSD and add an external HDD in a cooled case (my second choice above).