If you are using Aeroplan upgrade certificates for upgrading, the points earned should be 100% regardless of fare paid. This shows in the computer system as C-class, and C and Y fares get 100%. [Previously, upgrades got 125%, same as paid J, but this ended on December 31st.]

If you are fortunate to receive an Operational Upgrade, i.e. an upgrade without using certificates due to overbooking of the back cabin, you will receive whatever miles your fare was eligible for. Q, L or N will get 50%, V and above will get 75%. Y will get 100%.

If the gate agent makes a mistake in processing your upgrade, and it comes from the normal J inventory, then there is a chance you could get the class-of-service bonus, and thus receive 125%. This happens, but not often.