First I would like to suggest please use any framework, you will get most of the functionality in build.
Always create one parent class for your site and this class extends the Framework Controller Class,instead of extending that Framework class(Zend_Controller_Action) in every controller.
class UserController extends SiteController {}
class CategoryController extends SiteController {}
Now, you can put all common code of your site in SiteController ,
for ex: if you need to send mail to users the put sendMail() in SiteController so that every controller can access the same.
In Model :-
Same as Controller make parent class of each model.
create common methods like fetchAll(), delete(), deleteById(), getMaxId(), fetchById() ......
in parent model, in that way your models are almost empty..
Means they contain only dedicated methods associated with that particular Model.
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2. Functions used for ajax call need to start with ajax or any prefix so that you can easily figure out all the ajax methods in any controller.
3. You should follow Zend Naming Convention while you code.