Other than Yahoo!, which is quite frankly beyond the reach of many smaller websites, paying for your directory submission can be a waste of money. You can get just as good a resultfrom submitting to free directories, or those that are free with a reciprocal link. If the directory is exceptionally good, the cost is low, and your directory ranking will be improved by paying a fee, do so if you wish. Personally, I wouldn't recommend you pay for what you can get free elsewhere.
To start with on your submission campaign, in my opinion it is better to submit to those directories that will allow you to easily modify your listing. That way, you can correct mistakes and get your campaign down pat before submitting to directories that don't allow you to logon and modify your submission, thus saving yourself from wasting or reducing in value your efforts in those directories.

What Directories to Submit To
The best are Search Engine Friendly directories (those that actually have your site URL listed at some point, rather than outlinks that are simply code). Some will ask for a reciprocal link, some will not. One list of non-reciprocal directories is at http://info.vilesilencer.com/main.php?rock=seo-friendly.php. Opinion at the moment is suggesting that non-reciprocal or one-way links are better, although any relevant link is useful. Directories that encode their links are mostly useful for traffic if their Alexa Ranking is high enough. Directories that do not encode outgoing links will help your website's Search Engine Ranking.

Deep Linking
It can be worth linking to other pages on your site other than your main page. Before doing this, make sure that the directory you are submitting to permits you to both submit URLs other than your home page (some only allow top level submission), and for the same site to be submitted to different categories (not all directories permit what are essentially multiple submissions of the same website). This will work especially if you have online tools or directories (such as your links page) on your site that are useful and relevant to add to other directory categories.

Choose the Relevant Directory Category
Most directories will have many categories you can submit your site to. Decide on the one that is most relevant, preferably a keyword that you are aiming for high search engine ranking in, and try to submit to the same or similar category in every directory, at least for your main page (also see Deep Linking above). This will increase the ranking of your site relating to the keyword chosen.

Submit to Different Categories
If the directory allows multiple submissions, and your website is relevant in several categories, submit to all the relevant categories you can. This will increase the number of incoming links to your website. Again, carefully check the terms of any directory before trying this to make sure it is permitted.

Write Title
Write the title for your website. Try to include a keyword you are aiming for ranking in in the title, but make the use of it appropriate, don't just bang a keyword in for the sake of it; you could get your site submission rejected.

Write Description
Describe your website in a way that will attract visitors. The length of your description will vary from directory to directory, but most will be under 250 characters. Some will allow up to 1,000 characters, and in those cases write the most comprehensive description of your site and its features that you can. It is a good idea to write several descriptions of different lengths, say from under 50 characters for a brief overview, to around 150 characters for a fuller description, up to 250 characters for a yet more comprehensive listing, and finally a full description as previously mentioned for over 250 characters. Keep your listing pertinent to your website, insert keywords where relevant and appropriate, but do not just submit a keyword listing, as most directories will reject your submission. Save all your descriptions in a text file, and just copy & paste into the descriptions boxes when needed rather than typing the same descriptions out again and again.

Choose Keywords
Again, as with the description mentioned above, the amount of keywords you can use will vary from directory to directory. Some will not give the option, some will allow you numbers of keywords, whilst others go by numbers of characters. Make a list of all relevant keywords for your site, from most important to least, and basically keep adding keywords until either you get to the bottom of your list (unlikely unless your list is really short) or you run out allowed characters/keywords. Check what keywords your competitors are going for if you need inspiration. This can often be done by viewing the source of a web page and checking the META tags. Again, save your keywords to a text file.

Keep Track of Your Progress
Keep a careful record of what directories you have submitted to, and your progress. It is far too easy to totally lose track of what you are doing, which does not help your linking campaign at all. The best way is by using a spreadsheet, such as Excel, to keep track of your campaign. At a minimum, you need to keep track of the following: Directory URL, Directory Name, Date Submitted, User Login & Password for those directories that allow you to alter your details and Response (accepted/declined). Other categories can include: Directory Alexa Ranking, Directory Page Rank (this will be for the home page only), Referral URL (if the directory will improve your ranking for referring visitors) and any Notes. If you are using the deep linking and multiple submissions strategies above, also keep track of what other pages you have submitted to each directory. Make a seperate entry for each URL submitted. For example, your spreadsheet columns could go as follows: Directory Name, Directory URL, URL Submitted, Referral URL, Login, Password, Alexa Ranking, Page Rank, Date Submitted, Response. I would advise keeping the list in alphabetical order, rather than order submitted, as that way you can check more easily whether or not you have submitted to a particular directory.