I recommend two great tools:
Backup and Migrate: http://drupal.org/project/backup_migrate which backs up the database.
Contrib Toggle: http://drupal.org/project/contrib_toggle which disables the contributed modules with one-click. (doesn't yet have 'enable' though!)
These have certainly made the process easier. But what else is there? Have you any recommendation? I though I read somewhere about another module to help automate the entire process?
I hope that an auto-updating system will be included in to Drupal 7.
My biggest problem will soon be running many different sites with Drupal and then having to periodically spend a lot of time updating. One of the major benefits of CMS is so my clients run their own sites and I don't have to do it for them, but this convoluted update process for each site is time consuming and confusing. And, for the most part, running a multi-site setup is not going to work for my clients.
I can't tell you how many times I've been caught by disabling contributed modules that need updating before I downloaded the newer versions, then I'd have to go back to the module page to find out what they were, or worse, re-enable them so I could get the download links. It's very confusing for a newbie.
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