I've seen a lot of Tien Vs Krillen threads, but this is the first Yamcha Vs Krillen one I've seen. I thought it was a given that Krillen was the better fighter, even though he gets slapped around more.
Yamcha gives up fighting after the Cell Saga and really lets things slip (you can see that when his flying ship almost crashes in the Buu Saga and he does nothing to save the day) so if your talking about that period then its Krillen all the way.
In fact I can only remember him fighting on two other occasions. Back in the Saiya-Jin saga Krillen proved the better fighter, handling four Saibamen while Yamcha couldn't even handle one. And Yamcha took part in a fight against the Ginyu force which he won (not sure whether it was his increase in strength or the fact that the Ginyu Force had just been killed.)
So I think the fact that Yamcha has limited experience in real battles (Krillen has been in many more battles than him) puts Krillen ahead.