I would disagree with the notion that you shouldn’t use paid directories – they protect against spam entries, for starters (same with paid article directories).
Google still loves Best of the Web, and Yahoo!’s own directory – both paid directories that don’t accept every request.
There are a number of other good ones, I’d simply look them up in Alexa for the top sites as far as traffic – not always an indication of the best sites, but you at least know they receive traffic.
Other than that, I don’t personally bother with these links too much. If the reason to submit to the directories is for SEO benefit, there are much easier means than guessing which directories are useful – such as making sure to submit a sitemap in XML format to the major search engines, optimizing your on-page factors, doing proper KW research and pinging new content.
Beyond that, guest posting in your niche after establishing a relationship with others in your field, article marketing, RSS submissions and gaining quality backlinks by ensuring you have link worthy and SEO’d content is key.
I might be persuaded otherwise if there was an easy – EFFECTIVE tool to submit to directories, but I don’t currently have such software.
Submitting to DMOZ, About.com and ipl2 would be a great start (and in my case, END) to directory submission.
The other thing I’d suggest – check out your competition. Where are they getting links from? Check Yahoo Site Explorer and use those directories…