I tried to make Yojimbo work for me, but there were just too many problems with .Mac syncing. So, I moved all passwords and secure notes to Keychain Access that comes with OS X. I started a new keychain to store my stuff, and it syncs perfectly with .Mac since Tiger.
For everything else (i.e., PDFs, notes, scribbles, pictures, etc.), I went with Journler...a great, free (donation-ware) application that can also be used for your blogging needs in many instances. I gave the developer $10 for his work--very much worth every penny. It still has some problems, bugs, glitches, and quirks, but it's hard to beat the price.
Now, Journler has no .Mac syncing function. However, it's easy to use an Applescript or syncing application to keep your Journler items synced between computers, and it has a lot of features that Yojim-blow lacks. I'm sure the developer will add .Mac syncing later.