I've used Unision for a serious effort for some time.
And, indeed, it's only really useful for performing sync of two directories. When you get up to 3 or 4 systems your trying to keep in sync it becomes very tedious and very time consuming. Pretty much worthless, unfrotunately.
It's easier at that point to just use a rysnc script to sync everything to a central server then pull down the changes. Even then it becomes very difficult to delete, move, or rename files effectively. Basically it boils down to copying using rsync then manually carrying out delete/rename/move operations. It can't really be automatically handled unless your very clever at scripting.