Once you've eleiminated most of your bugs it's genaraly the environment that can cause the most trouble. Here's some off me head I've encountered during my daily grind.

If Mysql is down your DBI connection will break your script.
•Use an eval or try/catch when executing

File locking can cause problems
•use file control

Badly set up apache/Mysql
•Ensure apache timeouts, max number children etc are ok

System calls have the potential to break your script. Forking off multiple processes can help, when they fail your main process carries on.

Calls to various modules may also cause your script to break

Users can also cause bother with
Back Buttons
•use http headers to prevent caching

Proxy Servers
•Can interfere with authentication and sessions

Turned off features, Old Browsers and Apple Macs
• Cookies turned off unsupported etc