These are two quite-ish similar applications for the mac, both used to store info, pictures, links and a whole load of other stuff. I own both, buying Yojimbo first a couple of years back and then getting MacJournal when it had 50% off at the end of last year. I like both of them but have been using the latter more since I bought it. Having two loads of info in different bits of software is not probably ideal so I have been trying to move most of the stored stuff from Yojimbo into MacJournal of late. This has proven to be easier than anticipated and for the majority of stuff it has just been a matter of dragging and dropping entries from one to the other.
I guess I have grown to prefer MacJournal as I find it a bit easier to use and slightly more flexible. I particularly like the "Journal" feature of MacJournal for keeping a diary and the way you can "print" webpages or web receipts to MacJournal. This can also be done in Yojimbo to be fair and is a very easy way to get info into the software. MacJournal also lets you post entries to your blog without the need for an active internet connection so you can do posts and then save them as drafts and upload when a connection is available. Another useful advantage of MacJournal is its superior text editing features which allows you more formatting options and the ability to do entries as lists with checkboxes, for example.
I tend to use MacJournal for storing info, links to useful articles about bits'n'bobs, pdf's of software receipts and webpages, for keeping a daily diary and have all these things categorised. You can also add tags for easy and quick searching. Both are very good apps at what they do but I would have to give the nod to MacJournal as it just offers a bit more.