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As a first timer to 3D fractals, I found Mandelbulb 3D easy to get into and explore.  It was almost intuitive for me to experiment without needing to read up on what buttons do what.

Unfortunately that is not the case for Mandelbulber; I struggled trying to figure out how to get around.  Some buttons didn't seem to work like I expected or not at all.  Instead of researching and trying to figure out how to get around, (though I did for a while with no luck), I went back to M3D, or another fractal tool.

I am not putting down Mandelbulber, but it just hasn't been easy for ME to work with....
 

I love them both! I have 2 quadcore computers running all the time, with one program on each machine.
Different things I like about each program:
Mandelbulber:

• I like the ability to add backgrounds (though I wish they rendered at higher resolution - is there a way I'm missing?)
• I like the ability to easily make things glow
• I like stereoscopic rendering
• I like the ability to save as jpegs
• I like the control of the IFS fractals parameters - though I really haven't figured out how to use it well yet!
• I like the ability to run from command line - I hope to massively parallelize my rendering soon!

Mandelbulb3D:

• I like the ability to edit color pallets
• I like the ease of navigation
• I like the left and right arrows for rolling around the camera axis
• I like the ease of animation
• I like the ability to preview animations
• I REALLY like the bezier interpolation between keyframes

I know Buddhi's working on improving the interface in Mandelbulber, and the recent addition of the timeline is great progress. My biggest frustration with Mandelbulber is the interpolation between keyframes, which causes me to lose a bunch of time accidentally slamming into walls and cutting corners. Preview would help, but beziers would be better than splines!

One thing that's a bit challenging is to transfer a fractal from one program to the other. The folding parameters for the Mandelbox seem to be defined a bit differently between the programs, so I've not been able to easily compare exactly the same. No big deal though. 

In general, I am so happy and excited to have these awesome programs to play with and to create unbelievably amazing 3D fractal animations. ***THANKS***  Krzysztof and Jesse!!!

Absolutely love both programs.  Big props to both authors.  I'd say the biggest comparison/contrast between the two, for me, is that I use Mandelbulber more for still frames -- I love the lowmem rendering of large pics, and Mandelbulb3D for animations -- I find it easier to navigate, for the most part (unless I get myself stuck somewhere odd and can't get out...). 

I also have found that what I would think are similar settings produce different things, so I love messing with the settings in both, just to see what I can make.  I do like the myriad settings in Mandelbulber under the Kaleidescope IFS and Hybrid -- have made some truly weird things...partly because I have little clue what some of them do.    I need to dig out "Mandelball."  I've found it easier to do cut-away renderings in Mandelbulb3D as well as and pretty slick lighting options.

All in all, they're both amazing programs and you can't go wrong with either one...but both is infinitely more fun...so to speak.  Mandelbulb3D works very well under WINE, for the record, since Mandelbulber runs under Linux.