In my opinion, in a “perfect world”, a site could be navigated in any way the visitor wishes.
~ Thematically (by Category) ~ ideally in the manner / order the webmasters considers most valuable / important.
~ Via Sitemap ~
~ With search ~ And good search, mind you. Ideally, having indexed every word on the site.
~ Through sorting ~ via date, via last modified, via page title, etc.
~ By tags & “contributors” ~
Those are the ways that come to mind, and I believe are most common. Each with their own pros and cons. But if you have them all, I guess the cons don’t really matter. Obviously, that is quite difficult and certainly asking too much of (some) hobbyist web developers.
I organize my content thematically (by category). I acknowledge that it makes it difficult for the visitor to find what they’re looking for; to easily reach the things that interest them. But I see my site as art. I will organize it in a manner that best reflects that art. Dear visitor, finding the things you are looking for is important, but so is finding the things you are not.
I take great pleasure in navigating personal web pages. I can only go through so many in a day; I try my best to dedicate the time necessary to have felt that I properly explored another’s invested time and effort, their world, their message. Perhaps there is some value in encouraging people to take the time to slow down, in addition to improving navigation.
To anyone that perhaps find themselves consumed in this conundrum: your site is probably more important than its navigation, don’t let this stop or delay you from making it. Time is so valuable.