The question that has been puzzling me all day today was...
If I plug my SATA controller and hard disk in to a 16x PCI-Express slot will it make my disk IO faster?
Technically it should be faster because if you look at the logical block diagram in your motherboard manual you will notice the 16x slots are directly connected to the northbridge which on most CPU's now is now integrated where as the 1x slots will be connected via the southbridge.
To try to prove this I attached a 1Tb WD harddisk to a Lian-Li IB-01 5 port SATA controller to a 1x slot then a 16x slot and used HDTune to gauge the performance.
The results from the 1x PCI-Express slot:
The results from the 16x PCI-Express slot:
As you can see from the above the results are near identical.
So in answer to my days pondering it makes naff all difference whether you attach your harddisks and controller to a 1x or a 16x PCI-Express slot...
Now the second pondering this raised is was the bandwidth out of the harddisk the limiting factor...
I repeated the tests with a Crucial M500 240Gb SSD
the SSD attached to the controller in the 16x slot
The SSD attached to the 1x slot
Again the difference is not significant. (values bob slightly with repeated passes)
So in conclusion you may as well fill your 1x slots with SATA controllers and save your spare 16x slot for a second video card :-) if anything the 1x slots are slightly faster. I guess the PCI-Express lanes used could be being passed from the Northbridge to the Southbridge for processing thus introducing latency. But that's just a guess.