When using Microsoft Outlook with Exchange (not the online only mode) a Sync Issues folder that appears in the local PST folder. From the link above I know why it exists - but often that information is not needed (sync issues caused by the fact you are not on the network, and haven't switched to offline mode).
For users besides the space consumption, the fact there is a folder called issues with a big number next to it worries them. So my question is, what are effective methods of managing this? Can be server side (such as settings) or client side (such as rules).
If you do have a suggestion that is specific to a version of Exchange or Outlook please indicate that version.
If you're running Exchange 2007, look into the managed folders policy settings in the Exchange Management Console. It will at least let you manage automatic deletion of the messages that appear there. As for the folder itself, I wouldn't touch it. Outlook doesn't like it when system folders are messed with (not that I have tried on this one though)...
I'd be more concerned as to what is causing Sync issues to occur. As Trondh is saying, you can use Managed Folder Policies to force the deletion of these Sync issues, but that is not a very reliable option.
There are many kinds of different sync issues, but in Outlook 2003 w/ Exchange 2007, most of these are certificate related. If you do not have the appropriate certificates installed in the appropriate manner, then you will receive Sync Issues relating to your Offline Address Book (OAB). More than likely, you'll have an 0x8004010F error. A good place to start if this is the case is: http://msexchangeteam.com/archive/2007/04/19/437902.aspx, other issues could be related to your AV setup, etc. Without more information on what kind of Sync errors you are receiving, it's hard to point you in the right direction, but ignoring the sync errors is not the optimal way of dealing with the problem.
Outlook won't let you delete these folders, but they can be removed with OWA. There's no good way to remove them with a script, though. There's also no automated way to clean out their contents. Your best bet will be to train your users so they understand that the contents of these folders are a troubleshooting tool for you, not something they need to worry about.
the mailbox cleanup assistant will let you delete the conflicts from your HD