Now that is a really tough question, especially given it's such an eclectic bunch.
Let me take my best shot at answering:
I love the RC30. it's such a small, nimble bike with just the right amount of power. Transmission is sublime and still plenty of grunt. the Ergos are perfect and it's got great racing pedigree. I love the looks too after all these years.
The 888 fits a similar bill as the Honda but approaches it from a very different way. Sound is amazing and I love the design and again the power isn't overwhelming but just right.
As far as the newer stuff...The FE with race exhaust and SL wheels has so much character and is an absolute beast. It's ferocious in the best way. The new v4 is seductive in its own right because it makes you feel like a hero and enables mortals like me to explore new levels of speed. It's really, really good!
The Desmo could be my favorite, but just doesn't get enough seat time. It's clearly a special bike, but I'm candidly not well enough acquainted with it to know. (note to self: need to change this!!)
That brings me last to the 998R. If i had to pick one bike I would have to say this one is my favorite. It is such an amazing ride. it is so well balanced, incredible power, amazing soundtrack and sooooo smooth to ride. Looks similar to the SPS, but is so much more refined and is the pinnacle of this era for Ducati.
Each one of my bikes I picked up because I personally loved something about them and each shines in certain categories and some in many.
But there you have it. 998R it is!
But I reserve the right to change this opinion!