Considering the possible notes including enharmonics:
C D E F G A B
C# D# E# F# G# A# B#
Cb Db Eb Fb Gb Ab Bb
Is there a case when we use for ex. B# Major Scale, since B# is just C?
Same case for E#, Fb, Cb
===Update:
When creating scales to find the key signatures there will be scales that fall into that case mentioned above. See the grid of scales on the link: http://imgbox.com/xiBVsiuD
===Update 2:
Actually I believe I found the answer by re-checking the grid. ie: Valid Roots are the ones that are in the Grid!
Not sure if it really answers your question but I've never seen music written in the key Cb, B#, Fb or E#. No one writes in A#, D# or Gb either. It's unnecessary to have that many sharps or flats in a key signature when one with less (or none) will work. They exist theoretically but it's easier to read music in the key of Eb for example (three flats) than it is to read in D# with it's five sharps and 2 double sharps.
You will of course see these notes written on the staff and or used to describe a note in a chord, for example; in the key of F# a II major triad would be spelled G#, B#, D#.
As Ken mentioned, folks mostlyl use whatever is most pragmatic when writing in a given key. Th SCALE GENERATOR is very handy for helping to make all of the shapes of a given scale over the neck. One can play in key, or out of key or against, key, depending on what you are going for. MOre often than not, solos end up sounding better to most folks ears when they stay in key and bend to pitch. But that's just the start.
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