I have submitted my site to about 100 link directories, but I don't find that any of them appear when I use my Google Webmaster Tools to view external links to my site.

Do they help Page Rank?

I set one up myself actually (link in sig) to help myself an others with more inbound links, but if it's not helping with Google PR, it kind of seems like a waste of time, no?

Does anyone have experience with this?

Link directories are also known as link farms. Linking to link farms is not recommended since many of them may not be relevant in content to your site and will be rated accordingly by the search engine crawler.

So you should search for directories which are content specific then? Or not at all?

As far as I know, niche related directory submission will help to get more PR as well as traffic too. Specially, when you submit a site, if you can choose the right category that is more than enough too.

As an SEO expert I met once on an Amtrak train told me, "Becareful where you park your website. If you park it on a bad neighborhood, you may undesired results." This is very relevant to link directories. Becareful where you link to.

If you get a backlink without having to reciprocate, it shouldn't hurt you though in theory, right?

The backlink will help you especially if it is coming from a well respected site.

Choose the directories for submission which constantly indexed by Google and visible in search engine result pages. There is wastage of time if you add your resource to dead directories.

Relevant directory is very helpful to get visitors for your site.

Very helpfull for raise Page Rank.