I used both and still do for over 3 years now. as much as I wanted to consolidate all my content in one app, such perfect one still does not exist. I use Mybase as my primary, however. These are the pros/cons in a nutshell ...
Mybase
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1) most stable and performing app I have ever used. I have over 423MB of data in it and it NEVER crashed once or under-performed.
2) I have never seen an app that comes even close to MyBase when it comes to compression (zlib). Above data resides in a 10MB files after using compression.
3) It has 90% of the features you would expect from an information manager in the areas of capturing, sharing, organizing, and so forth.
Now, the not so great stuff
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1) support and development is slow (took over a year to release 5). You can tell from the forum activity.
2) integratoon with other apps is sometimes cumbersome if not dysfunctional e.g. outlook.
3) even thought MyBase SDK has been published for a while, i did not see any add-ons developed .for some reason, was not embraced as good as i expected.
4) can organize data at 2 levels only, tree and labeling system. Some user find this limiting. i did not.
5) limited RTF support specially tables. this is common for so many apps i have seen since they tend to use MSoft's controls. They shy away from developing their won or acquiring 3rd party ones due to cost or support consideration.
UltraRecall
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1) Uses the solid rock db engine sqllite. you get the full protection and reliability of such engine. I have at 5 DK apps that uses it and it never failed me. UR claim that db sizes can grow up to 2TB and still have an acceptable performance.
2) UR developers are very very distinct when it comes to programming and writing Dk apps. They are known for that in the development community.
3) Support is exceptional. They take it seriously and it shows on the forums.
4) Program strikes a clever and unparalleled balance between free form and structured data. You can tag your free content with system as well as user generated attributes. this gives you unlimited choices organizing, categorizing, and searching your data.
5) I love its content capture facilities. With UR3, you can (with click of a button) capture from MS OL, IE, FF, TBird. It also has a global capture key you can use from any app. This is so convenient and it works.
The not so great stuff
Despite the below issues, they truly stay on top of user and bug reports. they actively release patches (4 or 5 patches since the release of 3 in march of this year). This minimizes the impact on their user base.
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1) Program can and will crash more often than what i like it to. This week for example, it threw 2 unhandled exceptions and some cpp debugging messages.
2) RTF editing is badly limited. They provide 'limited editing' and if you want more, they allow you to open up the node in an external app like msword.
3) They implemented a feature where you can 'edit content externally' instead of the integrated RTF editor. i have seen at least 3 posts on the forums for uses complaining of data loss. I did experience it myself with both releases 2 and 3.
4) can only display the content of a single info item at a time. with MyBase, you layout content from multiple items in so many ways (using windows tile/cascade) functions.
I truly have not put UR to the test with large volume of data to tell about its performance. but so far, it has been performing great.
Again, there is not such an app when you can get all what you need. but between MB and UR, i have all my need satisfied.