Well, it's truly up to you... I mean, many people go for the Apache 1.3.x line because it has been out for much longer, and so the chances are that quite a few of its bugs have already been corrected. Sure, there will be many more, but that's the same as everything.
The thing is that 1.3 has been out for a while, therefore it is used by more people and tested by more. 2.0 is also very secure, and with its new features, any old fool might go for it, but as I already said - it's up to you.
Check out
Secunia to find out the vulnerabilities for Apache 1.3.x and 2.0.x. Read reviews on the 'Net. Have a look around this site.
It's up to you!
J_K9
Pssst...I used 2.0.x on my first time, but many people say it's best to go with 1.3.x...