...that actually degrade your PR instead of even being neutral , such as some Directories, submission services ?
Not really. Directories that promote themselves as "search engine friendly" can be safely ignored as a waste of money. That phrase is a tip off that they're in the business of selling Toolbar PageRank because their entire site is focused on web publishers, not on attracting site visitors. Thus, their focus will be on artificially increasing their Toolbar PageRank in order to make the directory marketable. Usually, sites like those are simply ignored. Which is why I answered "not really" to your question as to whether it will degrade your PageRank.
Stop thinking in terms of PageRank and think in terms of traffic. When thinking of link building consider who your visitor is and what sites they typically visit. This leads to discovering opportunities for obtaining citations.