Since the first publication of this post, a couple of packages have emerged to automate this process. The installr package for Windows and the updateR package for OS X are particularly good. However, this continues to be a popular post, so I have decided to keep it up. This work-flow is short, sweet, and cross-platform.

1. Before you upgrade, build a temp file with all of your old packages.

tmp <- installed.packages()
installedpkgs <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
save(installedpkgs, file="installed_old.rda")

2. Install the new version of R and let it do it’s thing.

3. Once you’ve got the new version up and running, reload the saved packages and re-install them from CRAN.

tmp <- installed.packages()
installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
missing <- setdiff(installedpkgs, installedpkgs.new)
install.packages(missing)
update.packages()

If you had any packages from BioConductor, you will need to reload those as well.

chooseBioCmirror()
biocLite() 
load("installed_old.rda")
tmp <- installed.packages()
installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
missing <- setdiff(installedpkgs, installedpkgs.new)
for (i in 1:length(missing)) biocLite(missing[i])

All done, now you can get back to cracking out R code. This method helped me save a lot of time, hope someone else finds it useful!