Honestly, in my time working with Apple and in communications/IT, most of the time MobileMe issues revolved around the user not understanding and syncing their devices properly. Almost all of the issues related to the users not registering their computer in the MobileMe settings, and not setting it to automatically sync the various features you need. As well, it's paramount to make certain that your main system is perfect in terms of contacts, calendar, bookmarks, etc as this will become your original "template". Once that is done, have MobileMe sync your information to the MobileMe cloud and replace all the data from the cloud. Then configure all your other devices/computers to pull that data from the cloud. I've often seen users configure their iDevices for their MobileMe accounts and chose "Keep on iDevice" when syncing, which can create duplicates and such. Taking these initial steps are crucial as they solidify your data and ensure that your devices will properly sync.
As HiRiz stated, do not check any of the sync settings in iTunes if you are syncing over the air through MobileMe as this will create duplicates. These issues typically involve consumers not understanding how a cloud service functions and assume it's simple. Unfortunately it's not for most, and it becomes frustrating to the user and eventually Apple is blamed for an issue that they are not responsible for causing.