I guess I would have to say that Professor Wurzle from the Bulumnia trilogy is my favorite character, with Jonathan Bing the cheeser as a close second, and finally Ahab coming in third.  Typical, I'm sure, but I love the way the professor is seen coming home with a bucket full of water plants so he can watch them grow.  I have a thirty gallon (113.7 liters) fish tank out in the garage that I have been dieing to set up in my basement so I can go and raid the local creeks and river of their plant life to see how they grow...  I never seem to have the time though.  

I like Mr. Bing for his laid back ways and fairly simple outlook on life.  I've been gathering up the courage to make a little room down in my basement where I can take a stab at making some of my own cheeses, but that's another project that will have to wait until I get a little extra time in my life.  I've found a recipe for a soft raisin cheese that I wouldn't mind trying out...  If that's a success, I'll be moving on to try and reasonably emulate Mr. Bing's raisin cheese.  A Pipe dream you say?  We'll see.

B.

Speaking of tanks, ponds, and Twomblians, if you go to:
http://www.loaches.com/species_pages/misgurnus_anguillicaudatus.html
and scroll down to near the bottom of the page, you will see a picture of my loach Sikorsky, named for the villainous dwarf. We currently have another loach named Selznak. Though alas gone now, we even had goldfish named Buffo, Gump, and Ahab at one time.

Someone should really negotiate the rights to make plastic Henny-Penny men for fish tanks.

The bad guys may not have been real in Mr. Blaylock's earlier books, but there was a few frightening scenes from the Disappearing Dwarf.  Headless boatmen rowing about the Tweet River, Goblins setting fire to their own heads (or was that Elfin Ship?), skeletons marching along the beach, and just imagine the old witch looking you straight in the face with her milky white eyes and cackling like there was no tomorrow...  I'm sure I would have immediately forgotten about any self dignity that I may have been clinging to and ran like hell.  

Oh, and let us not forget that Selznak/Sikorsky was a vivisectionist.  Thinking about that for a while could keep a person up late at night.

B.

Ha!  I was just remembering how wonderful the team-up of Rev. Bentley and Father Mahoney was.  The best part of All The Bells On Earth, I say.

I'm surprised not to see the name of Langdon St. Ives.  
Who wouldn't want to be Mr. Ives, I ask?  

Confident, always saving the world from destruction, successfully I might add.  He beats himself up for not being two steps ahead of Narbondo at any given time, and he's willing to risk it all for his one true love Alice.

He's not the most real of Blaylock's characters, but he's easily the most heroic.

I'll have to go with Andrew Vanbergen from The Last Coin. You've got to love a guy who obsesses about finding Wheetabix and travels cross country for it, without bothering to step inside a local grocery store first. Maybe love isn't quite the right word, but it sure made for a great story. Jules Pennyman has to be my favorite villain.