I am using the Email class in Codeigniter, and in the manual I see that there are 3 protocols that can be used: mail, sendmail and smtp.
What is the dfiference between mail and sendmail? Is it true that using mail protocol will have a higher chance of having the domain marked as spam?
If you're using *nix, chances are mail() and sendmail() are identical. mail() will still use sendmail, but it passes any arguments you have defined in your php.ini.
The bigger difference is between SMTP and sendmail. If you are doing a lot of mass emailing you want to use SMTP because sendmail opens a new connection for each email which adds quite a bit of overhead.