Open iTunes, go to advanced and look for a menu choice for Authorize Computer. If you only see it say "Deauthorize Computer," go ahead and select it. Then, go back to the same location and choose "Authorize Computer." This almost always takes care of the problem. Otherwise, there is a chance you have moved (or somehow your computer has moved) the music files from where they originally were. Look for a song that is on iTunes, but not your iPod. After you have found one, try to play the song in iTunes. If an ! appears next to it, it is because the path for the song is no longer valid. If you are using a Mac, open finder and enter the name of the song or part of the name and hit enter. It will find the song file. If you are using Windows (poor you) then click the start button, and select Search, and once again input the name of the song. Likely, all of the missing songs have been moved to a similar place (not likely the same place), but pay attention to the path, and look to see if more songs are there. After you determine where your songs are, go to iTunes and click File>Add Tunes to Library, then select all of the songs that need to be added to the library (you will have to input the path). To prevent this from happening in the future, open iTunes, click iTunes (File on a PC)>Preferences>Advanced and select "Keep iTunes Music Folder Organized."
The real pain in the neck is that you will need to delete the broken links from iTunes. It may be easier to delete all files from iTunes, and import everything over again. That is what I have done, but you do lose your playlists if you do this.