Superficially the two apps appear to be very similar: both allow you to store and preview documents, web archives and bookmarks, create notes, etc; both KIT’s groups and Yojimbo’s collections work more like iTunes playlists than regular folders, where a file can exist in more than one group at a time and there is no hierarchy.
However, Yojimbo has special formats for things like passwords and serial numbers while KIT will work with any kind of file including images, movies and even formats it can’t preview. KIT keeps all the originals as files on disk (or uses aliases to link to existing files), Yojimbo keeps everything in a database. Some people prefer one approach to the other, so that’s cool.
In a nutshell, KIT is more about files, whereas Yojimbo is more about data. At times, the feature sets of the two collide, but that could apply to any number of applications in this genre. I’m actually very happy about Yojimbo because when I released KIT back in 2004 it offered a fresh approach that not everyone seemed to understand. That changed after the release of Yojimbo and interest in KIT renewed, so it’s certainly done me some favours there.
In the future you can expect to see KIT further differentiate itself for Yojimbo. I have some very exciting plans for the app, some of which will be seen sooner rather than later.