I use a HR monitor and track my rides with Garmin Connect, Map My Ride, and Strava. Using the same data, they give a pretty wide range of results. As a general rule, MMR gives the highest estimate, running as much as twice the others. Garmin and Strava are usually closer to each other, so I use the most conservative if the two.

Alternately, most people burn 30-40 calories per mile, so it's not that hard to compare MMR's numbers to a rough estimate of what they should be.