Truthfully, it's one of my *least* favorite things to do...but it's worth working it in - I try to count it as part of my marketing efforts (for the forums) so it gets done.
I've done alot of manual link submissions for clients. Quite a few times I've submitted to nearly every directory in the 'free' list at Directory Critic
(1,000+ dirs) it get boring but pays off in the end.
One tip: set up a sep. email at your domain *just* for links, it brings a TON of spam in.