If I want to create a custom key combination to run a command, are there any keyboard shortcuts reserved for this? I always find it difficult to decide on which shortcut to override because I'm not sure what commands I shouldn't override and which commands plugins I may install in the future will try to set.
Also remember that all of the reserved sequences can trivially be used as prefix bindings, if you want to group related tasks together, or simply want to take maximum advantage of a particular easy-to-type C-c<letter> sequence.
For instance, I use C-cm as a prefix for some of the magit (and related) functionality I want quick access to. e.g.:
(global-set-key (kbd "C-c m m") 'magit-status)
(global-set-key (kbd "C-c m l") 'magit-key-mode-popup-logging
(global-set-key (kbd "C-c m b") 'mo-git-blame-current)
And of course, C-cmC-h then shows me all the bindings I have under that prefix.