Well, this is a hard question because, of course, it depends on your niche. Generally speaking, there are a few key aspect you should pay attention to, before deciding to spend some money (usually a few bucks) to submit your website to a paid web directory.

Now, people expect valuable things for free and maybe that's why free web directories had their time of glory. Those directory owners wanted more and more listing so they accepted (and some are still accepting) any kind of website, therefore making that web directory a piece of... junk. Yeah, that's the truth, no matter how harsh it sounds: why would you, as an owner of a quality website, want to be listed among tons of gambling, duplicate content, MLM, MFA and pharmacy sites? We can call that directory... "useful"? Noppe, that's right.

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Now, there are also the so-called paid web directories. Let's get this straight: they aren't called "paid" because they want your money in order to list your website. We talk about the so-called "review fee" which doesn't guarantee that your listing will be accepted (if your website will be rejected, usually you get you money refunded). In order to make something valuable, all responsible webmasters need time, various investments, a reliable server, technical support and so. It is not easy to open every suggested website, analyze it, move it maybe into a more appropriate category, edit the title and description etc. This is the sole reason why most of the "good" directories will always charge you a review fee.

After you have a list with the "best web directories" (in your opinion), try to spend a few hours and check several things out. From my 10 year experience, based on the numerous marketing strategies I developed and the articles I have read, these are the top key factors you should take into account:

1. Domain age. This is simple, it is like wines, the older the better. Why is that? Because it is a well-known fact that search engines tend to give more authority (importance) to 2-3 years+ domains. Many newly created websites are sand boxed, many young webmasters want fast results and they tend to destroy a website with duplicate content, link exchange strategies etc. A good way to check a domain name's age is by checking out when it was registered (at it's domain registrar) or by using a tool.
2. Alexa ranking. The Alexa ranking is somehow trustworthy because it shows if a website has any visitors. It is obvious that the lower the Alexa ranking is, the better. Look after web directories with Alexa values lower than 400-500k.
3. Penalized by Google or not? Just so a site:example.com in Google's query bar. If there are no results, or only the homepage is popping up, then it's obvious that there is something fishy about that website.
4. PageRank of the category pages. Most of the web directories will advertise that their home page is PR2-5. But your listing won't be listed on the homepage, but on an inner page, a category page. If a website is well-built the homepage should have the highest PR value, then it should decrease as you dig into the pages. For example, my web directory's homepage is PR4 and all category pages are PR2-3.
5. Loading fast or not? This is not something to worry about, but I would not submit a website to a website that loads in 20 seconds.
6. Link popularity. Does the website have a decent amount of incoming links? You decide what is decent.
7. Content. Most web directories will only have the listing and their description as primary content. In my opinion it is a good sign if from time to time you see new content (like articles, blog posts etc) on a web directory.
8. The quality of the already listed websites. Browse thru the categories of a web directory and check out the quality of the titles, descriptions etc. If it doesn't look like spam to you, then you're on the right track.
9. How long your will listing stay included (if accepted). As I already wrote in a blog post, it is annoying to charge an annual fee for a listing. It is not worth it (maybe except for Yahoo's directory and Business.com). Look for web directories that will keep your listing included forever.

These are the main indicators I look after when I submit a website to a paid web directory. I am not saying that this is the "directory submission Bible" but you'll see that every responsible webmaster will agree with me on these factors.