Red rows in the library mean that the file is not shared. For incomplete files, sharing means that the file is eligable for partial file sharing (PFS). A file being shared via PFS will not be found by normal querying methods, but is instead shared only through the "download mesh". When you download a file, you insert yourself into the download mesh. As other clients download a file, they try sources that are advertised in the mesh.

The download.dat (download.bak being an automated backup of download.dat, used when LimeWire senses that .dat is corrupt), as stief mentioned, is an index into your incomplete files. It keeps track of exactly what byte-ranges have been downloaded for any given incomplete file. If an incomplete file is not listed in download.dat, then it will not be shared through PFS (and will be listed in red in the library).