You don't say what command-line you use. I don't believe I have had a problem when trying to archive a whole directory + contents, eg:
tar cjvf /tmp/g1albums.tar.bz2 /var/www/albums
If you did something like the following, I can see why it didn't include "dotfiles":
tar cjvf /tmp/g1albums.tar.bz2 /var/www/albums/*
The * doesn't match dotfiles as they are considered "hidden files" in unix. If you *really must* do it this way, something like the following should work:
tar cjvf /tmp/g1albums.tar.bz2 /var/www/albums/* /var/www/albums/.??*
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I use rsync over ssh to copy from one server to another (in this kind of case) a la:
rsync -avxHPe 'ssh -x' /var/www/albums newserver.example.com:/tmp/g1/