As a directory owner I'm sure a priority for you is to spread Google PageRank to your internal pages, and also to start to rank internal pages of your site, not just the homepage. However, it is easy to look at big sites like Digg, Yahoo or CNN, and assume a similar layout is good for you. Let's go over a few things you might want to consider for your strategy:
Important Note #1: We are talking about internal links and external links. We highly recommend you should get an actual count of all links. You might be surprised!
Now if you have a pagerank 5 or higher site, having a few more links on the homepage is probably a good idea, because it will visibly spread much easier. However, if you have a pagerank 4 or less site, and you have 50 or more links on your homepage, you may find that getting pagerank to internal pages is a nearly impossible task.
Let's also discuss categories. A smaller directory with just 10 high level categories should be sufficient. There is no rule that says you must also display subcategories, and if you are just getting started displaying 30 or more categories may be a recipe of pagerank reduction on your internal pages. So we would advise you to grow your site slowly, and don't start out linking to tons of categories on the homepage. It wouldn't be wrong to start off with a mere 5 categories and do a great job with those.
Important Note #2: When we talk about pagerank, we are not just talking about search engines. We are talking about increasing the chances that users will arrive on useful pages of your site!
A common problem with directories that use a "category dump" where they pre-load their directory with categories is there are tons of Stub Pages. Google doesn't tell you the exact percentage, but as pagerank spreads through a site, there is a "bleed off". Let's say you had a pagerank 4 page with one link on it. Technically, that would mean you are passing that pagerank 4 to the next page at 100% strength. But with the bleed off, it ends up being less, for example, maybe it is 75%. So as pagerank spreads your site, 75% becomes 50%, etc, so quickly your pagerank can disintegrate. When you have a bunch of pages with little or no content (ex. empty categories), you are wasting pagerank on pages that are not going to benefit you.
So bringing your focus back to quality instead of quantity can have a wonderful benefit in that you have more pages that are valuable from the homepage, and they start to show a visible pagerank.
Important Note #3: Quality Content wins every time.
So here is a "prescription" you might want to try:
1. See what you can do to reduce the number of links on your homepage
2. Then make it your task to make sure that every link that someone could possibly click on the homepage takes them to something valuable.
3. Your top level categories should be pages worth visiting
Once you are successful with these first steps, you'll be well on your way to building a special directory that people enjoy visiting. Good luck!
If you have questions or comments, feel free to continue discussing internal pages and pagerank here.
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