Starting from PHP 5.3.9 there is a brand new php.ini option: max_input_vars. You may read in the PHP documentation about it. But what you don’t probably now is that if you are using the Suhoshin patch (for example if you’re using dotdeb packages), then you need to tweak 2 other variables to increase the max number of POST variables accepted by your PHP.
So, if you want to increase this number to, say, 3000 from the default number which is 1000, you have to put in your php.ini these lines:
max_input_vars = 3000
suhosin.post.max_vars = 3000
suhosin.request.max_vars = 3000
The other suitable option is to fix your form and make it saner :)