Pipes & Tobaccos magazine featured a great write-up of Twain in their Fall 1997 issue, there's a picture of several receipts circa 1880 from Salomon & DeLeeuw where along with buying a dozen or two corncobs, he'd buy Blackwell's Durham by the pound.
It seems Blackwell's Durham is the most likely candidate, but I don't think he limited himself either.
A couple of quotes:
"No good smoking tobacco in Europe - no Durham, Vanity F, Lone Jack - but I brought mine with me..."
"Gave away all my Durham & kept the worst brand in America - still it was of course better than any in Europe - Latakie is almost as good."
...and the thing about his filling technique is from an interview by Luke Sharp who sez
"I was much impressed by the ingenuity with which Mark Twain fills his corn-cob pipe. The humorist is an inspired Idler. He is a lazy man, and likes to do things with the least trouble to himself. He smokes a granulated tobacco which he keeps in a long check bag made of silk and rubber. When he has finished smoking, he knocks the residue from the bowl of the pipe, takes out the stem, places it in his vest pocket, like a pencil or a stylographic pen, and throws the bowl into the bag containing the granulated tobacco. When he wishes to smoke again (this is usually five minutes later) he fishes out the bowl, which is now filled with tobacco, inserts the stern, and strikes a light."
another good thread on a similar topic here: