I use webalizer with crond and a script that calls seperate config files for each domain.
Like this: webalizer -c domain.a.conf webalizer -c domain.b.conf webalizer -c domain.c.conf and so on..... Then use custom configs for each domain. I will note each domain needs its own logfile but you should be doing that anyway. Maybe not the best or most elegant method but it works for me. I am doing it this way with about a dozen domains. Tom