Hello

As far as I know Nepomuk use only "blacklist" way to choose which file should or should not be indexed. Now I want to index only files with some particular extensions. Is it even possible without adding to blacklist all other extensions/mime-types and names of files without extensions? It's much of work and every new file without extension is new trash in indexing result.

Unfortunately to the best of my knowledge, Nepomuk does not support whitelisting extensions instead of blacklisting.
You will need to file a feature request in this case.