The best practice is to find some way to implement your feature that does not require patching the original core. You should try to read -  http://drupal.stackexchange.com/questions/59054/why-dont-we-hack-core 

Anyway, if you still want (or need) to maintaining your Drupal Core with a patch you can use any of this projects to manage your patches.

 - https://github.com/davereid/drush-patchfile

> This project seeks to solve the following problems:
> 
> - How do I document what patches I've applied to a project?
> - How do I reliably know what patches are applied or not without manually checking every single one?
>- How can I be reminded that I need to reapply a patch after downloading a module update?


 - https://github.com/xendk/bandaid

> Drush tool for helping with patch management on Drupal, which helps
> with patching, and upgrading modules.