Personally, I try to avoid the use of eval(). Many languages, like C++ and Java, don't have a function like eval(), and yet they are very useful. So it's my theory that if a script uses eval(), the script can be redesigned to NOT use eval().
Anyway, coming back to your question, I generally make a file called common.php, which includes functions that are general for a website - like error display functions, database functions, etc. So basically I suggest your method 3.
Diego