1-Color of paper.
Nobuteru Yuuki always does his gengas on 
salmon pink paper. However, if he does layouts,
they will be on regular paper and you cannot
tell.

Not all character designers use their own color
paper.

2-Episode. Look for episodes where the character
desginer is also the animation director.
Note that yellow paper is always the animation
director.

3-Doujin genga collections.
Yup.  Some animators will publish collections
of their genga. 
I have on of Seikai no Monsho, and that's how
I can tell that a cel I own was based off a 
genga that chara designer Keisuke Watabe drew.