This function will give the Y position of the text cursor (caret) when it is in a contenteditable element. This particular one only works on CKEDITOR.

Get caret Y position in HTML (WYSIWYG) editor from document origin.

var getCaretYPosition = function(){
    var editor = CKEDITOR.instances.editor1, //get your CKEDITOR instance here
        sel = editor.getSelection(), // text selection
        obj = sel.getStartElement().$, // the element the selected text resides in
        range = editor.getSelection().getRanges(), // range of selection
        container = range[0].startContainer.$, // get the DOM node of the selected text, probably a textnode
        textlen = typeof obj.textContent === "undefined" ? obj.innerText.length : obj.textContent.length, // get the length of the text in the container
        offset = range[0].startOffset; // get the offset from the beginning of the text in the container to the caret
    if (container.nodeType === 3) { // if the container is a text node
        while (container.previousSibling) { // add the length of all the preceding text nodes and elements in the same parent element
            container = container.previousSibling;
            if (container.length) {
                offset += container.length; // this is for text nodes
            } else {
                offset += container.textContent ? container.textContent.length : container.innerText.length; // this is for HTML elements
            }
        }
    }
    var pct = textlen > 0 ? offset / textlen : 0, // the percentage of the caret position
        cursor = Math.floor(obj.offsetHeight * pct); // multiply elem height by percentage of carets position for caret's offset in pixels

    while (obj.offsetParent) { // add all the offsets of all of its parents to get the complete offset of the caret from document origin
       cursor += obj.offsetTop;
       obj = obj.offsetParent;
    }
    cursor += obj.offsetTop;

    return cursor;
}

Brilliant !
This is far better than this other method i saw : insert a empty "fake" element, get cursor position (i.e. fake elt position), then remove the fake element.

Thus, like the other method, there is some problem with selecting text with keyboard (shift+arrows) :

The correct Y position is achived only when selecting UP.
When selecting DOWN the top postion of selection is given (instead of the bottom wich would be better)
Also : selecting over blank lines make gives false cursor position

Would you know how to make it work ?