by fretboard knowledge you mean learning the notes?
if so:
start with 1 string at a time and you speak out loud the intervals between notes -just the harmonic notes- ) then 1 fret at a time (fret 1 all 6 notes, fret all 6 notes...) then 1 note across the fretboard (all positions for A, B...) etcetc
fretboard practice:
"fretpro" (freeware)
scales knowledge:
"fretpro" (the same as above)
"guitar alchemist" (freeware)
"guitar scales method" (shareware)
music reading: (just found this one so I'll try it tomorrow)
"gnu solfege" (freeware)
a website:
chordfinder :
http://www.jazzguitar.be/guitar_chord_finder.html
the useful feature (to me) is that it gives the intervals between the notes.
ear training:
www.miles.be