srdiamond, first of all, please keep in mind that this review was only the first of hopefully more roundups for this software category. It is a very difficult category to cover comprehensively, and knowing that from the beginning, I purposefully didn't worry about covering everything in one roundup. Otherwise, I would've freaked out and lost my mind. That being said, let me respond to your comments
I am puzzled by the consensus that favors MyBase and Surfulator, yet complains of the difficulties managing large trees. Considering the problems users experience with trees, you would think that the leading programs would provide solutions. There are two solutions available, netheir well represented among the reviewed products. Since users want a usable tree, programs that make trees more accessible deserve a close look. One of the requirements for managing a large tree is the ability to move multiple headings simultaneously. Multiple selection in the tree is one basic property of modern outlining programs, and almost none of the trees have this capacity. Ultra Recall provides this modern outlining feature in its tree, in its most advanced incarnation, which it calls logical linking. This means topics can be subordinated to multiple headings (cloned).
Actually, Surfulater has the capability already to clone notes. The default action for copying/pasting notes results in cloned notes, not two copies of the same note. Mybase can't clone per se, but it can link to other notes, meaning that you can create a note that when you click on it, it will jump to the note that it is linked to. Not exactly the same as cloning, but functions similarly.
As for managing large trees, that is a topic that his been discussed extensively in this forum. There was a long discussion about how the trees were inefficient and that better methods exist such as categorizing using keywords or tags. A couple of programs do this, like Evernote and Zoot. The author of Surfulater has mentioned putting tags into the program in the future. Mybase also has the ability to "label" notes which is like tagging them with keywords. MyInfo also has an interesting way to tag notes (mentioned in the roundup). The thing is, neither solution is definitively better than the other. In some cases, the traditional hierarchy works better, and in others, the more virtual tag-based system works better. I feel that the simple hierarchy starts breaking down as the database becomes larger and larger, but for smaller databases, the hierarchy works well. Not all people are going to have an enormous number of notes, and the simple hierarchy may feel easier, simpler, and more familiar to them. Remember, not everyone is going to be a "poweruser".
As for UltraRecall, I remember trying it out and it seemed to have lots of features, but a bit too bulky for a simple notetaking program. I'll try it out again. Maybe the cloning of notes and multiple note selection is the deciding factor for you in choosing the right program, but you have to be careful not to make one little feature the focus of a general review of a broad category like this. With me, my favorite feature is the search-as-you-type feature (like in Evernote), but I purposefully make sure I don't make that the defining feature of notetakers.
Another program that allows creating a tree with multiple selection--this one, unlike UltraRecall, definitely definable as a "notetaking program"--is ndx Cards.
On the other hand, perhaps the tree isn't the best way to go about organizing notes. Then programs that use keywords exclusively and in a slick fashion might be the ticket. Here PersonalKnowbase, which has good notetaking features, thought not as good as ndx Cards, should be considered.
I will take a look at those programs and add them to the next roundup. Just from a first glance, ndx cards seems to be unconventional about it's note organizing, which may be very efficient, but also may present an unfamiliar interface for users. But I'll say more when I have messed around with it a little more.
As to the process of creating a single note, Microsoft OneNote can't be beat. It has outlining within notes (that no other program currently in development has) and adapts to inputting notes in a variety of ways.
OneNote was a gross omission from the first roundup and will definitely be included in the next roundup. It is clearly a popular and important software in this category.