I usually create an excel workbook with separate sheets for directories (the big one being ODP/ dmoz.org), search engines, industry portals as most often, you'll find loads of relevant ones for your site, and competitor backlinks. I submit to the directories, SE's and portals and then check my competitor's backlinks and where I appropriate I try and get my site added as well. HTH
Had a funny happen this week. I had just about completed the last couple of pages on a new domain, I paid up for the domain name and pondered my submission strategy .... only to look up and see google was already giving the site a good spidering ..
I can only assume Google picked up on the new registration at whois, or wherever?!?
There is a little note in the Google "info for webmasters" saying it doesn't matter how often you sumit (fat lot of good it'll do you!), and I've read so many times that over submitting a site will get one banned ... which to believe ;)?