I have an iPOD Video 5th generation and an iPOD Touch 3rd generation with the same problem. There hasn't been an iTunes update for the iPOD Video in quite some time, so I can rule out later versions of iTunes as the culprit. However, I do sync both iPODs to iTunes regularly. The skipping over certain songs problem is probably occurring each time the iPODs sync to iTunes, but I don't notice it until I try to play a specific song and it is skipped over, even though it played fine many times before. The songs will play from the iPOD from within iTunes when the iPOD is connected to my PC, but they will not play when the song is clicked on from the iPOD touch screen or wheel.
On previous occasions, I have found that if there is an ampersand (&) in a song title, it will be skipped over. On one occasion, I converted an MP3 that was skipped over to an AAC and that solved the problem. I have also found that deleting anything in the comments section of the MP3 Info solved the problem. The most common solution I have found is to delete the skipped over song from the iPOD and then load it back on through my iTunes library. I think the issue is file corruption during the iTunes sync process, because all of the songs that are skipped over never had a problem playing on either iPOD previously. The problem occurred with two such songs again today, but it only occurred on the iPOD Touch, which would make sense if it was a corruption issue during a sync. The fix today was to delete the skipped over MP3s on the iPOD Touch and copy them back over to the iPOD Touch from the iTunes library. Unfortunately, there is no way of knowing whether another MP3 was then corrupted during the sync, until you try to play that song and it is skipped over. This could be a never ending process, because we don't know the source (software, cabling, hardware, USB,etc.) of the corruption.