Q:

How to Harmonize uncommon scales?

How do you harmonize scales like

C C# F F# Bb
Whole tone scale : C D E F# Ab Bb

?
(The scales above are just examples.)
Scales like these do not seem to bias to Major or Minor harmony, right?
What chords do you use/hear when these kind of scales are used?

A:

A short simple answer could be the same as for any scale: You use the notes of the scale to assemble chords!
This is at least what you do in jazz;
Say, for example, that you have a jazz melody that (for the passage you are harmonizing) uses the notes of a C mixolydian b9 b13 scale (C Db E F G Ab Bb). Then you can use chords built on the notes of that scale such as for instance C7(b9b13) or Bbm9, but you can't harmonize with for instance chords as C6/9 or Bb△7 since these chords contain notes that are not in the scale that is used in the melody.

But I believe more data is needed from the question. Are the scale notes the only ones allowed or available, or are actually other notes available to use for the chords? -- For example: Harmonizing with only the five notes of a pentatonic scale will give you a very different result than when you use a pentatonic scale in a jazz blues context where you actually have other notes available for harmonizing (and thus the scale, in some sense, is actually not only a pentatonic).

A:

The whole tone scale is generally associated with the augmented chord (+5 triad or +7 or 7#5, in the jazz notation). 
Your first "scale" is not really a scale. C7sus4 b9 #11 matches, but so do does Bb -7 9 b13 / C
You'll get a large set of examples in the Scale Syllabus (http://www.jazzbooks.com/mm5/download/FREE-scale-syllabus.pdf). 

