Even though commercial web directories might be in decline, I've mentioned several times that general knowledge web directories from the university and librarian communities (aka human built) are doing a great job creating and maintaining useful tools for the web directories for the researcher. Yes, they might be small (in terms of total entries) versus other tools but the quality of each source included in the directory is what's most important. Very library like.
This SearchDay article: The Value of Non-Commercial Web Directories introduces a few of my favorites including the LII, Infomine, and the Resource Discovery Network.
Remember, libraries which are often compared to web engine databases are NOT the same thing. General web engines take whatever they can access and toss it into one large database. Libraries are controlled collections, built one resource (print or electronic) at a time after reviewing the quality and authority of the material, determining if the material is needed, and reviewing how the item fits into the overall collection. In other words, building a great collection is a skill and something that librarians take much pride in doing. Networks are also in place to allow a library users to gain access to materials not in their local collections.