One of the things I find most important about tagging via Spotlight comments in OS X is being able to have some kind of index of the tags you use. I'm a huge tagger of stuff on del.icio.us, but they've kind of gotten out of control, with a massive tag cloud (*choke*). I recommend setting up some kind of system, be it a text file as an index, of the tags you use that you can at least somehow reference.

I also use Devon Think and use directories. Haven't gone to a non-directory format, but there is an "unfiled" directory I use with a ton of crap in it that I may never just use.

Am personally on the fence with DevonThink Pro and Yojimbo. I love that Yojimbo has Spotlight integration -- the idea of it, anyhow -- though I've never had to use it. However, I enjoy aspects of DP over Yojimbo -- particularly how customized I can make the UI, how pop-up windows remember their sizes from one to the next, etc.

One thing that I've also done with system tagging in OS X is to add tags to calendar events and my address book. To do so, I make sure my tags all have some kind of unique prefix, like @clients or something. Doing a query in Spotlight then brings up not only files, but contacts, events, etc. Great way to relate items together across multiple applications.

Haven't tried the folders solution that akr95 mentions -- frankly, I think one thing DP and Yojimbo are good for over this menthod is creating web archives. There's no tool I know of in OS X (and I'll now look) that allows you to create web archives of this sort as "files" you can drop in a standard Finder directory.