Here are some places that might help
There are really two things to learn:
First, given a postion on the fret board, name the note. Go to
www.wholenote.com, and on the home page, find the "Name that Note" game in the Learning Tracks box. (While you are there, look up Lesson 458, Learning the Notes Across the Frets. The lesson suggests making flashcards to carry with you so you can grill yourself about notes, strings, and frets.)
Also, go to the "Trainers" section of Ricci Adam's Music Theory site, MusicTheory.net. An exercise on that page highlights a string and fret, and you have to name the note. (There is also a note trainer.)
Second: given a note name, locate the places on the fretboard where that note can be played. I haven't run across web trainers for this function, since the computer doesn't know what note you have played in response (at least, my computer doesn't). In a way, this second thing falls out of reading music, since written music gives you the notes to play. If you want to learn to read music at the same time as you are learning the fretboard, go to
www.familygames.com and dowload the free NoteCard program. The program presents a note on the staff, and you have to click the fretboard on the string and fret where the note is to be played.
Most people learn the top two strings (and the frets near the nut on the top two strings) first, since the root notes on the chords we play, and since they are reinfoced as we play chords. Those things you cram into your head that are not reinforced melt away, and have to be re-learned. Since I play mostly rhythm and don't practice sight reading at all, I have that kind of "top-string" knowledge of the fretboard. Even though I can map out the notes as desrcibed by other posters, the way it becomes useful is to apply it, as Chris Shaeffer described in his post.
(I play rhythm mostly, but have learned a few scale patterns. They are moveable, and work in my mind in relation to a starting note. So if I know where to start a scale, I can jam, playing the whole scale without knowing which notes I am playing. So, when you get tired of memorizing the fretboard and want to actually make music, if you know some scale patterns you can jam. What I am saying is that naming the notes is not the same thing as making music, but obviously they are both related.)