There is no way to discover how all apps are being used in a comprehensive manner - each app does different things, and in some cases, providing passive functions where the only way you would know if someone has used it is by increasing the logging to a non-performant level, or monitoring access logging.
Some can be partially discovered by scanning configuration. From your list 1, 3, 5, 6, and 8 are partially or wholly discoverable from their config, but for the rest, your only option is to go through the config manually, or ask the users who might be using them.
To cover the discoverable ones, get a trial of my company's Microscope - it can give you reporting on how a lot of your apps are configured. I know that's a blatant advert, but it's a good tool for this (and you can always not buy at the end of the trial)
As for replacement(s), another advert - Scriptrunner can directly replace 6 of your apps, and partially replace "Time to SLA" if you're only using parts of its functionality.
I don't know of a replacement for "Links explorer" that wouldn't cost similar or more, without you having to make large changes to the way you work.
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