I do not believe that a single backup application is the best because it does not not know the specific gritty application details however a general purpose backup application is great for all of those miscellaneous applications. Use an OS specific backup app to backup the OS because there seems to be hidden files and files with extra "this file cannot be read". Database have to have their own backup software to ensure transactionally correct backups.
Oh yea, also make a separate small "in case of emergency" backup which can be used to create a minimal system to start the recovery process.
A multiapp method is way more work but the single applications do not seem to have the documentation that I would like see and understand that the application provider has thoroughly tested the app. For example try to get a list of files which the backup application does not backup.