Options are the value which can be used for mostiny storing settings value. We also can say, It is the value similar to config variable. Which can be use any where in the site and will be same for all the objects.
Whereas Custom fields are only for posts, and its values are store as meta. So Its value will be different for all the post. Or we can say its kind property of each post.
In Short, Global values are store as Options
and values related to Posts are store as Meta.
Hope this will help you.