What is the difference between calling sys.exit() and throwing an exception in Python?
Let's say I have a Python script which does the following:

open a file
read lines
close it

If the file doesn't exist or an IOException gets thrown at runtime, which of the options below makes more sense?

no except/catch of the exception, if exception occurs, it fails out (which is expected behaviour anyway)
except/catch the exception, logs the error message, throw customized exception by myself, fails out.
in an except IOException block, exit with an error message e.g. sys.exit("something is wrong")

Does option 3 kill the process while 1 and 2 do not? What's the best way to handle the Python exceptions given that Python doesn't have a checked exception like Java (I am really a Java developer ^_^)?
sys.exit raises a SystemExit itself so from a purely technical point of view there's no difference between raising that exception yourself or using sys.exit. And yes you can catch SystemExit exceptions like any other exception and ignore it.
So it's just a matter of documenting your intent better.
PS: Note that this also means that sys.exit is actually a pretty bad misnomer - because if you use sys.exit in a thread only the thread is terminated and nothing else. That can be pretty annoying, yes.
Difference between calling sys.exit() and throwing exception