What is the main drawback of a mind-mapping program? Try to make a circular connection, it's something always some kind of workaround and not on the same level with the standard connections. Mind maps are essentially tree-shapes. concept-maps don't have this restriction.
i don't know how they programmed it, but cross-references are more or less "created equal". This and the automatic layout makes it a good program to use for things that are interdependent.
the bad thing about this program is the pricing scheme. the free version leaves you without printing and exporting which makes the free version a complete trial or vendor-lock-in version.
the pro version is too expensive for a person not using it to earn money with it , so it is to expensive for a student arranging the thesis or a person just entering their knowledge and saving it in a flexible, interconnected way. a lawyer, detective, advertising guy or any other person connecting various informations may find it reasonable to pay more than $200 for a program that has a narrow scope but fills that purpose better than others.
as an alternative (true concept-mapping and not the hierarchical mind-mapping) to "the Brain" i suggest cmaptools,
yed graph editor is neither mindmapping nor conceptmapping tool, but it can be tweaked into such.

That's true, it's not really a mind map. But I don't think it's a drawback. Thanks to the possibility to have any item "thought" as your central thought, you can focus on it and see everything directly connected with it. If you need to see the big picture, there are possibilities like outline view and expanded view (the first being very good to see hierarchy in the system, the other is a kind of mind map, where you can change the position of each individual thought).

The problem with the mouse oriented interface was solved with the release 5.5, where you can set your own keyboard accelerators to almost any command.

There are some thing I don't like on PersonalBrain (for example you can't make links directly from item notes to another item, or I miss the possibility to make a nice list of items arranged according to some attributes) but whenever I tried to find something that would fit me better I landed back on PersonalBrain after a while.

And BTW with the nice dynamic interface it will be a lot of fun to organise your stuff and go through it.

Give it a try! (there is a free version without some features, but very useful anyway.

I haven't bought this software because:

1. You can't manually order nodes.
   Considering the main aim of the product is to tame masses of information, this is a major downfall.
   It's also despite the fact that this feature is the third most requested one as of writing. (I think this was also a problem 10 years ago when i first tried it)

2. People have lost data on it (something about a java upgrade) - which would be disastrous for the only use I would ever consider paying for

3. It's very expensive - starting at $150, for features that are fairly necessary for any serious use. Given point 2, the price is hard to justify. Given point 1, I can't use it any price.

4. Other commenters are right that it is a bit hard to get a grip of all your info at once.

Having said all that, it's one of the most intriguing pieces of software I've ever seen!
Such a shame about the other points.

This is true, but remember that if any item becomes the central topic, this can result in limiting the scope of items viewed to those immediately related to the item - quite a limiting factor IMO. Using PB is a bit like shining a torch around a room in the dark - it only shows a small fraction of what's there. Mind mappers show large, detailed maps whose items don't jump around the way they do in PersonalBrain's display, which can be disorienting. Because the displayed spatial relationship of items changes completely with each new central item ("Thought") the user may find it difficult to create a mental "map" of his database. Hence PersonalBrain should not be confused with mind maps.

PersonalBrain as an application shows a lot of potential, but IMO this has a long way to go before it is comfortable to use, even though it has been around for 10 years. Its interface is highly mouse-oriented, so can be very inefficient at times, particularly to keyboard users. The manual omits a lot of important details, making it a difficult application to learn to use well, and once you get to know it you start discovering many gaps in its features which have not been implemented despite being requested by many users for years.

It can handle relatively large information databases but is held back by inadequate capability to manage such databases.

Looks like a great program but at $200+, it seems overpriced for the consumer market.