For changing the back plane you might look at the Pro Cable 1 with a review here.
There is also the DX 4 if you want to really stuff you Mac Pro with drives.
I don't have direct experience with a controller but was leaning toward a MAXPower RAID mini-SAS 6G-1e1i since it has both internal & external SAS ports. Note that this card will not boot the Mac Pro.
The real problem is that I would want both a RAID card and a Mercury Accelsior and the Mac Pro (2008) only has 1 free x16 PCI 2.0 slot and you would need 2.
There is also a rumor of a Mercury Accelsior with eSATA ports in the near future.
YES, it's definitely worth it. With my setup, sustained transfer speeds were roughly 75% better using SATA, vs. USB3.
I tested both configurations using ZoneBench as follows:
SSD: 120GB OWC Mercury Electra 6G
Mac: Late 2012 Mac Mini, 2.6Ghz core i7, model ID Macmini6,2, 16GB RAM
Hot-Swap unit: StarTech USB3-to-SATA dock, model SATDOCK22U3S ver2
All speeds are in MB/sec (mega-bytes per second)
Configuration A: SSD connected via Hot-swap USB 3 Dock
Lowest / Avg / Highest R/W speeds: 95 / 150 / 185
Configuration B: SSD installed in internal HDD bay in 2012 Mini (direct SATA):
Lowest / Avg / Highest R/W speeds: 145 / 250/ 460
All tests were repeated 5 times at intervals of 1 hour, under normal system usage. (A few apps open & idle, CPU & system I/O load 99% idle.)
As one can see, in this configuration, taking the trouble to mount the SDD in the Mini's internal SATA bay is well worth the massive performance gains.
Best Answer
This is the proper cable:
http://www.cdw.com/shop/products/Adaptec-Serial-Attached-SCSI-SAS-external-cable-1.6-ft/1217280.aspx
Details: