I am using Geeklog v 1.3?. Some of my pages have certain variables set, but others don't. They all use a master header.thtml, and although I believe there is a setting in the template code that ignores undefined variables, I think I have it set correctly.
The option for unknown variables can have one of three values: "keep" (so that they show up when not set), "remove", and "comment" (i.e. keep them as comments in the HTML source, but they won't be visible).
The default it "remove". However, that will only come into effect when you call the finish() method for a template. We had a few places in Geeklog (until recently) where we called parse() but not finish(), and so the undefined variables were not removed.
Okay, maybe I misunderstood your question then. Are you trying to define your own variables? In one of Geeklog's templates or in one of your own?
To add your own variables to (some) of Geeklog's templates, there's the CUSTOM_templateSetVars function (in lib-custom.php), but that was only introduced around Geeklog 1.4.0.