The newest version of Yojimbo now uses Wasabi Sync to do Mac-to-Mac syncing. Lex Friedman has the whole rundown.
Yojimbo is an app I used just about every single day from early 2009 until late 2012. Here’s my review of the app — which is still relevant today — from shortly after version 2.0 shipped.
However, last fall my collection of website bookmarks and notes reached a point where I could no longer quickly find something by search. It was with sadness in my heart that I decided to export most of my data out of Yojimbo and into type-specific apps and services. Bookmarks went to Pinboard; notes went to Simplenote/nvALT; and passwords, serial numbers, and encrypted documents went to 1Password. You can read about how and why I moved away from Yojimbo here.
What excites me about Yojimbo 4.0 and this massive time investment to get sync working, is that it shows Bare Bones has not abandoned the app. And if they’ve taken the time to implement syncing now (with hints and also getting OTA Mac-to-iPad syncing working), then perhaps there is more down the road for Yojimbo (such as an iPhone client, better searching, and who knows what else).