My vote was Martha, hands down. First, you have the whole unrequited love aspect, and the fact she was always following in Rose's shadow. Although she had the greater good in mind, you know she roamed the earth in order to try and score points with the Doctor, to no avail - is it any wonder she said "no more" afterward? And during that year she had incredible pressure because she was the only one who could save the earth and everyone she loved (including the Doctor).
Rory, on the other hand, had an opportunity to prove his love, he knew Amy was coming back because he trusted the Doctor, and if there was any real competition between the two for Amy's affections, volunteering for 2000 years is one way to one-up the Doctor, big time. And, ultimately, Rory gets the girl - and regains his humanity later. A win for Rory on every level I can think of.
So Martha was the harder done by, by far.
Alex