We recently made some changes in 3dANOVA2, which has been already distributed in the most recent version of AFNI package.
One significant modification is the simple effect testing in one-way within-subject (or repeated-measures) ANOVA: the -amean option for type 3 in 3dANOVA2. It is explained in the following page:
http://afni.nimh.nih.gov/sscc/gangc/SimEff.html/
Another modification is the contrast testing in one-way within-subject (or repeated-measures) ANOVA, which involves options -adiff and -acontr for type 3 in 3dANOVA2. The details can be found:
http://afni.nimh.nih.gov/sscc/gangc/Contr.html/
We are also trying to make some similar changes to 3dANOVA3, and to add options for 2nd-order contrast testing which is currently absent. The update will come out soon.
Gang