You can use this free search engine submission tool
to submit to multiple search engines at once. It does work, it's the exact same as manually submitting but at least this way you don't have to visit each site and it saves some of the tedium.
You should still submit your site using Google webmasters so that you can control more elements of it, but this works pretty well for non-Google/Bing search engines.
You'll need to enter in an email address to confirm some of the directories or search engines it submits to, so make sure you have one on hand.