I have many custom wordpress page templates and I want to keep them in different folder. Like /pages/
But, the problem is when I keep them in different folder other than the theme folder, the custom page options disappear from wordpress page template menu.
How can I keep the page templates in different folder and still access them in wordpress page templates menu ?
You want to use a child theme.
http://codex.wordpress.org/Child_Themes
I actually found you can in WordPress 3.1+, at least, just store your custom pages in folders. they still display in the long list on the editor page, but do allow you to sort them into groups, for space saving, it's handy to keep the folder names short.