The reason why I am suspicious of the tag approach and the reason why I have so far systematically disabled nepomuk on all my systems (in spite of being a long time kde user), it that I really feel that this approach is 'imprisoning' some of my data, taking control of it away from me.
1) This tag approach appears to be completely unstandardized and unportable between desktop environments. If I spend time tagging my stuff and one day later I decide that I like gnome/ubuntu/xfce better than kde, all this effort is lost.
2) Looks like there is no possibility to sanely export or share this metadata. If I have a bunch of photos and I organize it by means of sensible path names (e.g. Photos/2011/Summer), and I decide to share them with a friend, simply zipping the folder and sharing the zip file will give to the receiver not just the content, but also the organization. If I put all my photos in Photos and I rely on tags for the organization, there is not tool capable of making a container file (zip like) with both the content and the organization.
3) Looks like there is no possibility to rapidly control what gets tagged and how, particularly if one relies on automatic tools to generate the tags, like indexers. For instance, if some password file of mine gets indexed by nepomuk, I would like to assure that such data is immediately removed from the indexes, but there is no way to do it.
4) There is almost no control on the amount of resources that is used for the tagging, particularly when the tags rely on automatic tools like indexing for their generation. With nepomuk, if I disable automatic indexing for a directory, I do not see the space taken by the database immediately decrease. The database seems to only augment in space over time, which is even more worrying for tablet like devices.
5) There is no way to automate operations on tags. Say that I have a bunch of photos, and that I have organized them by paths. Say "Photos/2011/Summer". Then I realize that this is wrong, and that they should have been "Photos/2010/Summer". Fixing this is as simple as a directory rename. How do I tell a tag based system something like "Please select all Photos that have the "Summer" tag as well as the "2011" tag and change the "2011" tag into "2010"? I have the same problem with gmail labels. Not that the thing cannot be done, but is extremely more demanding in terms of time than a directory rename.