Servers need patches to be run, and on many operating systems, those patches require reboots. So that is one category of down time. Many companies schedule reboots from patches for low use times, such as Sunday morning. If there are no patches, they reboot the servers anyway at the regularly scheduled maintenance time (this is a hangover from the NT4 days when certain counters overflowed every week and a half, so rebooting weekly prevented other bugs).
One company I worked for had an e-commerce site back in the late 90s that brought in more than $1,000,000 in sales per month. Someone promoted the wrong tax table to the production database server. The cure was to restore the db server from backup, and apply the transactions since the last backup. This took several hours, during which the website was unavailable to take orders. Since the orders portion and the static sales brochures were running on the same site and were inseparable, both had to come down.
One company I worked for had some wrong text inserted into the wrong place and the CEO flipped out and had the website taken off line "for maintenance" while the layout and text were "fixed" and the appropriate victim blamed and fired.