know if the last cron run automatically or manually?
I'm not sure why you really want to check this. However, I can think of a few methods:


Alter the admin/reports/status/run-cron menu router item, and add some flagging to mechanism to detect the call. If the user runs cron through this page, that's definitely a manual "Run Cron" call. Implement hook_menu_alter, and change page callback (probably file and file_path aswell) to your own function. In this function, add some flagging mechanism, and run previous page callback. It's unlikely that another module will need overwrite the page callback so you are almost safe. A little performance hit during menu rebuilds.
Add your own cron handler, and check $_GET['q'], or better, $_SERVER['PHP_SELF']. 
For $_SERVER['PHP_SELF'], if it's index.php, that's a manual run. Otherwise it will be  cron.php, which is likely an automatic call. However one could click the URL containing the token, which is not actually an automatic. I think this is the best method since it does not need to assume other modules does not need to override page callback. A little Performance hit in each cron run. 
Hack the cron.php (better yet, copy it to a new file). For example, copy cron.php file to scron.php, and make your crontab request that file instead of the the regular cron.php with token. You can then edit the scron.php file, and right after the bootstrapping, add a custom code to flag the cron that the file is about to execute is an automated one. Requires some custom effort that you can't do with a regular hook_install implementation. Performance wise, this will work almost same since there are no any hooks involved.