I like working with checkboxes, more than with headlines with a TODO keyword.  Unfortunately, right now checkboxes  are lightweight and so do not enjoy all the privileges enjoyed by headlines - especially clocking in and out (which is very important for me). I wish that regular checkboxes were also allowed to have the same privileges as headlines. Has this idea been discussed before? Were there any decisions one way or the other.

Another option is to have checkboxes on headlines (which I find very intuitive). On one of Sacha Chua's blogs I found a defun to allow cookies to update checkbox count on a parent headline cookie if there were checkboxes on it's subtree headlines. This was given in one of her chapters in her new book that she had posted online http://sachachua.com/notebook/wickedcoolemacs/wc-emacs-07-managing-your-notes.pdf

So I took that and modified it *slightly* - (it had a bug whereby if the item after the subtree list was at the same level as it's parent's parent, the checkbox count would get confused and still keep on counting)... Still there are a few issues.

If anyone is interested, here is the code...
;;;_. Update Checkbox count - to allow for checkboxes to be used in headings
;;; Based on code from Sacha Chua
(defun wicked/org-update-checkbox-count (&optional all)
  "Update the checkbox statistics in the current section.
This will find all statistic cookies like [57%] and [6/12] and update
them with the current numbers. With optional prefix argument ALL,
do this for the whole buffer."
  (interactive "P")
  (save-excursion
    ;;declaring and assigning values to a whole bunch of variables
    (let* ((buffer-invisibility-spec (org-inhibit-invisibility))
           ;; assign point to the "beg" variable and
           ;; returning an error in case of error
           (beg (condition-case nil
                    (progn (outline-back-to-heading) (point))
                  (error (point-min))))
           ;; make a marker which will point to the end of the current outline region
           (end   (move-marker
                 (make-marker)
                 (progn (or (or (outline-get-next-sibling) (progn (goto-char beg) nil))
                            (progn (outline-end-of-subtree) (point))
                            (goto-char (point-max)))
                        (point))))
           (re "\\(\\[[0-9]*%\\]\\)\\|\\(\\[[0-9]*/[0-9]*\\]\\)")
           (re-box
            "^[ \t]*\\(*+\\|[-+*]\\|[0-9]+[.)]\\) +\\(\\(\\[[- X]\\]\\)\\|TODO\\|DOING\\|DONE\\)")
           b1 e1 f1 c-on c-off lim (cstat 0))
      ;; if called with a prefix argument, "all" will be non-nil; in which case count the checks in the whole buffer
      (when all
        (goto-char (point-min))
        (setq beg (point) end (point-max)))
      (goto-char beg)
      (while (re-search-forward re (marker-position end) t)
        (setq cstat (1+ cstat)
              b1 (match-beginning 0)    ;set b1 to the beginning of the recent search
              e1 (match-end 0)            ;set e1 to the end of the recent re search
              f1 (match-beginning 1)    ;set f1 to the  position of the 1st paranthesized expression
              lim (cond
                   ((org-on-heading-p) (or (outline-get-next-sibling) (goto-char (point-max))) (point))
                   ((org-at-item-p) (org-end-of-item) (point))
                   (t nil))
              lim (marker-position end) ; right now setting lim to the same as end - not sure what the above line is trying to do
              c-on 0 c-off 0)
        (goto-char e1)
        (when lim
          (while (re-search-forward re-box lim t)
            (if (member (match-string 2) '("[ ]" "[-]" "TODO" "DOING"))
                (setq c-off (1+ c-off))
              (setq c-on (1+ c-on))))
          (goto-char b1)
          (insert (if f1
                      (format "[%d%%]" (/ (* 100 c-on)
                                          (max 1 (+ c-on c-off))))
                    (format "[%d/%d]" c-on (+ c-on c-off))))
          (and (looking-at "\\[.*?\\]")
               (replace-match ""))))
      (when (interactive-p)
        (message "Checkbox statistics updated %s (%d places)"
                 (if all "in entire file" "in current outline entry")
                 cstat)))))
(defadvice org-update-checkbox-count (around wicked activate)
  "Fix the built-in checkbox count to understand headlines."
  (setq ad-return-value
        (wicked/org-update-checkbox-count (ad-get-arg 1))))