Here's something I came across:
Comparison of Postures from Pen and Mouse Use
I'll post the summary, since the PDF is quite long:
Results from the Wacom pen test demonstrated less posture deviation from neutral during pen use
than during mouse use. Mice studies have demonstrated excessive deviation from neutral.
Excessive hand pronation and extension, as well as ulnar deviation and radial deviation have been
observed of subject using mice. No pronation was observed of subject using the Wacom pen.
Although extension and flexion was not measured, it was observed in only one subject who used
the left hand; but the extension and flexion of this subject was not excessive nor prolonged.
Average ulnar deviation during pen use was substantially less than during mouse use. Radial
deviation for both pen and mouse use has been demonstrated to be low, but average radial
deviation with pen use was less than with mouse use. In conclusion, pen use results in a posture
more neutral than during mouse use and thus appears to be a biomechanically superior input
device.