The Pioneer Anomaly has been solved May 29 2012
I missed this last July when the news came out, but since I've been following the Pioneer Anomaly for the past eight years, I wanted to mention it here for closure purposes. First, what the hell is the Pioneer Anomaly?
The Pioneer anomaly or Pioneer effect is the observed deviation from predicted accelerations of the Pioneer 10 and Pioneer 11 spacecraft after they passed about 20 astronomical units (3×10^9 km; 2×10^9 mi) on their trajectories out of the Solar System. Both Pioneer spacecraft are escaping the Solar System, but are slowing under the influence of the Sun's gravity. Upon very close examination of navigational data, the spacecraft were found to be slowing slightly more than expected. The effect is an extremely small but unexplained acceleration towards the Sun, of 8.74±1.33x10^-10 m/s^2.
A team at JPL has tracked the problem to uneven heat emissions from the probes' fuel source.
For their new analysis, Turyshev et. al. compiled a lot more data than had ever been analyzed before, spanning a much longer period of the Pioneers' flight times. They studied 23 years of data from Pioneer 10 instead of just 11, and 11 years of data from Pioneer 11 instead of 3. As explained in their new paper, the more complete data sets reveal that the spacecraft's anomalous acceleration did indeed seem to decrease with time. In short, the undying force had been dying after all, just like the decaying plutonium.
A more recent paper by the same researchers offers even more support for their theory. Case closed, I say.