Skype chat is definitely the weakest link the chain for our remote team as well; it's basically unusable beyond a handful of groups. We've been migrating over to IRC for as much as we can. We also briefly toyed with using Mumble (http://mumble.sourceforge.net/) for voip, and while it was pretty compelling in terms of cross-platform stability it never really took off in our organization.

The article mentions only moving off Skype if it's sufficiently advanced beyond Skype. IRC by itself is not, but we've got our own IRC server that adds some important features like indexing and catchup: http://writequit.org/blog/?p=444