I have 25k miles on my TCH. I have a spreadsheet with all of my gas receipts and a log of what my MFD says my mileage was. I've also used the same pump at the same station for probably 90% of my fillups.
The issue here is precision and accuracy. Wikipedia has my favorite diagram (shots on a bullseye target) that explains the difference:
http://en.wikipedia.org/wiki/Accuracy_and_precision
Over 25k miles and 46 fillups my hand calculations are going to be accurate. But the MFD is much more precise.
In my case the MFD reads 1.2 MPG high.
All of my calculations are based off the odometer. Which I'm sure isn't 100%, but it applies to all calculations equally.
To get really good numbers the EPA uses a dynomometer to indicate miles driven and they measure the tailpipe for CO2 output to indicate how much fuel was consumed.