I've been using Subversion (the base of SVK), with only one irritating issue.
Package upgrades lead to the old version of the package being moved into a package-name.bak (.bak.2, .bak.3, etc.) directories. This move takes the .svn directory with it...so version control breaks everytime there is an upgraded package...subversion doesn't handle such things very gracefully, and refuses to update, commit, or anything else until such issues are resolved. I've had good luck copying the .svn directories into the package-name directory and sub-directories (yes, you have to get every subdirectory too), but it is rather a nuisance.
I'm not sure how to work around it, without removing packages from version control...which might be the right thing to do, and only add my own packages and customized packages to version control. Though that brings up the problem of not having an easy way to roll out a new server directly from the revision control, which is kind of a core part of how I've handled migrating my OpenACS instance from a devel server to a production server and then instantiating a new devel installation on the production machine. It's been very convenient to be able to check out the whole bundle of the site as it is right now and have a new instance running identical everything in just a few minutes.
Anyway, I imagine SVK has the same issue, since it uses Subversion for many of the low-level components of the system.
