Here is a re-posting of a walkthrough (Oct. 2007) of how to control for anticipatory baseline effects experimentally. Looking at it today, there are two things I would do differently. First, I would use random slopes for subjects and items. Second, I would use permutation tests rather than the quasi-logit approximation. Re-running the code today with an updated lme4 package gives me drastically different results than what I got in 2007, which worries me.
I hope to post soon about a new R package I have developed (gmpm) which enables estimation of p-values for an MLR model using permutation tests. If you want to try out the new approach, install the package gmpm from R-forge like this:
install.packages("gmpm", repos="http://R-Forge.R-project.org")
Then have a look at the kb07 walkthrough (just type ?kb07 at the command line).