Evernote is cumbersome for me, but where do people save the multitude of snippits from websites they visit and don't want to forget?
Now, those have been mostly replaced by similarly named folders and I just use wget to save pages & their files into the appropriate category.
The text files still hang around though for little chunks of interesting code, part names/numbers, references, and similar tidbits that do not need any media to go with them.
Occasionally I start new ones, as interests change. When I do, the old files get renamed or deleted. I've got various "notes" text files going back 20+ years, and because they're in plain text files (or html + images), I don't have to worry about services shutting down, proprietary formats changing, etc. It's a system that has been working very well for me, and I don't see any need to change it.
However, I do recognize that this works for me because I do not use a bunch of different devices, so I don't care about syncing, or using my method from mobile devices, etc. If you have those use cases, you'll very likely be happier with something else.
I've never used a Wiki as you described it - can you tell me more about your system?
The cross-linking itself is done directly in files. I use org-mode[0] in Emacs for keeping notes. No web access (one day I may some up but I have no pressing need), mobile mostly through Dropbox app itself (there were some mobile apps for org-mode files developed recently that aren't crap, but they're still geared mostly towards the TODO-list features, and I need a general-purpose org-mode notes editor; I haven't found any for Android yet). So I mostly interact with the Wiki whenever I have a computer with Emacs handy (at work I selectively sync wiki/ and several other folders from my personal Dropbox).
A very simple setup, but the real value comes from just storing all those notes over the years. I store everything and anything - from personal information I just can't remember for life (like social-security-bank-insurance-tax-whatever something ID), through cooking recipes, my geek code[1], dieting notes, shell snippets, notes about geopolitics, travel checklists - you name it.
[0] - http://orgmode.org/