This post is directed at guitar players, all other instruments can safely ignore it.  It's a quick 5 minute lesson that will result in your knowing the whole neck if you practice about 5 minutes a day for 5 weeks.

In teaching, I've found that one of the biggest obstacles for guitar players is learning the notes that they're playing.  It impedes reading skills, chord knowledge and construction, analysis and comprehension, etc.
You can learn a lot by studying shapes on guitar, but at some point you just have to know all the notes on the fretboard.

This can seem like a daunting task: after all, there are six strings with 12 notes each (assuming that you can at least identify the 12th fret and higher as repeats of what happens in the first 12 frets), making for a total of 72 notes to learn (compared with 12 on a piano or most other instruments).

Fortunately, it's not as big a task as it seems at first.  You just have to break it down in a manageable way. 
Here's how I learned all the notes on the guitar:

1) First of all, you only have to learn 5 strings, because two of them are E strings and have the same notes.  So already we've cut the total information to be learned down to 60 notes.

2) You don't actually have to learn all of the notes on the fretboard to know all of the notes.  You only have to learn the  "white" notes, i.e., notes that are white keys on a standard keyboard and thus don't require accidentals in written sheet music: CDEFGAB.
From there, the "black" notes are obvious.  Since you only have to learn 7 notes per string, we've now reduced the total amount of information to 35 notes, which is less than half of what it seemed like at the start.

3) The "white" notes have a pattern.  Learning the pattern makes learning the notes much easier.  How do you identify a C on a keyboard? It has a white key to the left and two black keys to the right.  If you can learn to 'see' that pattern on the guitar fingerboard, then you are halfway to knowing the notes.
From C: W W H W W W H (W=whole-step, H=half-step).  So there are two "natural" half-steps among the "white" notes.  Learn where those are on each string. Since you know that the notes in between are all whole steps, you can start internalizing the pattern.
So you can make a good start with learning the location of the 2 half steps on each of the 5 strings, which is only 10 pieces of information.  Much easier than 72!

So here's the practice routine:
work on one string a week for 5 minutes a day.

on each string, first locate the BC half-step and the EF half-step.  Play only on that string and play only those notes, saying the notes to yourself as you play them.
When you can do this comfortably (for most students it seems to take about 1-2 minutes the first time), then try to play up and down from the open string to the 12th fret and back, using only the 'white' notes, and saying them as you play them.
When you can do that comfortably, you can try to improvise, again using only the 'white' notes.  It's very important that you don't use any 'black' notes!  You are internalizing the pattern at this point, and anything outside the pattern will interfere with that all-important process.

Repeat this, on the same string, every day for the rest of the week.

Next week, start with another string and do the same thing. On the 7th day of the week, make sure to spend some time reviewing the string from the previous week.

Do the same for the remaining strings.

In five weeks, you will be amazed to find that you simply 'see' all the notes on the fingerboard, without even thinking about it.

You're welcome!

PS. By the way, this lesson was heavily influenced by ideas presented by Mick Goodrick in "the Advancing Guitarist', which is an amazing book.

UPDATE!
I've made a graphic to help visualize the white note patterns on the neck.