Every system needs temporary folders that any user is able to read and write BUT these directories should not be able to execute programs or scripts. Though this will only protect you from somebody running the script directly it will help with a large portion of the automated rootkits and trojans that script kiddies use. They will still be able to put the files on the system but they will be unable to execute them and create the back door. One of the biggest problems is php injection via apache in which people will have apache download and then run an exploit. Securing the temp directories is probably the single biggest thing you can do towards securing your server.
FAQs/HOW-TO's related to Linux and/or BSD server administration.