Why has Snow Leopard screwed up my Safari and my desktop's ability to stay organized
Sounds like you did an upgrade, perhaps with the help Migration Assistant?

Best way to deal with it?  Back up your data, and either
i) create a new account, pulling your data back in, but with a fresh library and settings or, better yet,
ii) reformat, re-install OS and create your account again, from scratch.  Pull the data in manually.

Upgrading, and/or migration assistant, often doesn't go well when automated.  Just the nature of the beast. If you're not entirely comfortable doing this, get a pro to do it.  Trust me.