I am using SharePoint Server 2007 + Windows Server 2008. I want to know whether there are any existing best practices or tools to maintain a SharePoint server, for example how to monitor SharePoint Server issues and backup SharePoint Server application (both code and data)?
Here is some info on MS TechNet that covers some of the options and the limitations of each: http://technet.microsoft.com/en-us/office/sharepointserver/bb736212.aspx
I would read through that and figure out specifically what you would like to do and how often you need to do it. For a system of any size, I really like what some of the third-party tools provide for backup and recovery with item-level granularity.
Here is a book I would recommend if you are really intersted in digging deep: http://www.amazon.com/SharePoint-2007-Disaster-Recovery-Guide/dp/1584505990
In addition, here is an aritcle with some key concepts I covered in a few presentations about creating a DR plan: http://nextconnect.blogspot.com/2010/02/keys-to-establishing-disaster-recovery.html