How to make all org-files under a folder added in agenda-list automatically?

Just naming the directory should be enough. For example this works for me very well:

(setq org-agenda-files '("~/org"))

Also take a look at org-agenda-text-search-extra-files; it lets you add extra files included only in text searches. A typical value might be,

(setq org-agenda-text-search-extra-files
      '(agenda-archives
        "~/org/subdir/textfile1.txt"
        "~/org/subdir/textfile1.txt"))

Caveat: If you add a file to the directory after you have started Emacs, it will not be included.

Edit: (2018) To include all files with a certain extension in the extra files list you can try the following function I wrote sometime back (a more recent version might be available here).

;; recursively find .org files in provided directory
;; modified from an Emacs Lisp Intro example
(defun sa-find-org-file-recursively (&optional directory filext)
  "Return .org and .org_archive files recursively from DIRECTORY.
If FILEXT is provided, return files with extension FILEXT instead."
  (interactive "DDirectory: ")
  (let* (org-file-list
         (case-fold-search t)         ; filesystems are case sensitive
         (file-name-regex "^[^.#].*") ; exclude dot, autosave, and backupfiles
         (filext (or filext "org$\\\|org_archive"))
         (fileregex (format "%s\\.\\(%s$\\)" file-name-regex filext))
         (cur-dir-list (directory-files directory t file-name-regex)))
    ;; loop over directory listing
    (dolist (file-or-dir cur-dir-list org-file-list) ; returns org-file-list
      (cond
       ((file-regular-p file-or-dir)             ; regular files
        (if (string-match fileregex file-or-dir) ; org files
            (add-to-list 'org-file-list file-or-dir)))
       ((file-directory-p file-or-dir)
        (dolist (org-file (sa-find-org-file-recursively file-or-dir filext)
                          org-file-list) ; add files found to result
          (add-to-list 'org-file-list org-file)))))))

You can use it like this:

(setq org-agenda-text-search-extra-files
      (append (sa-find-org-file-recursively "~/org/dir1/" "txt")
              (sa-find-org-file-recursively "~/org/dir2/" "tex")))

Edit: (2019) As mentioned in the answer by @mingwei-zhang and the comment by @xiaobing, find-lisp-find-files from find-lisp and directory-files-recursively also provides this functionality. However, please note in these cases the file name argument is a (greedy) regex. So something like (directory-files-recursively "~/my-dir" "org") will give you all Org files including backup files (*.org~). To include only *.org files, you may use (directory-files-recursively "~/my-dir" "org$").

There is a simpler way of doing recursive search of org files (courtesy @xiaobing):

(setq org-agenda-files (directory-files-recursively "~/org/" "\\.org$"))

EDIT: You can also filter out certain directory from lookup by adding a array filter. Example, filtering out all org files in xxxx/xxx/daily/ directory:

(setq org-agenda-files 
      (seq-filter (lambda(x) (not (string-match "/daily/"(file-name-directory x)))) 
       (directory-files-recursively "~/Notes/roam" "\\.org$")
       ))

For Emacs <25, you can use find-lisp-find-files:

(load-library "find-lisp")
(setq org-agenda-files
   (find-lisp-find-files "FOLDERNAME" "\.org$"))