Here's the prologue to The Adventures of Huckleberry Finn.
IN this book a number of dialects are used, to wit: the Missouri negro dialect; the extremest form of the backwoods Southwestern dialect; the ordinary "Pike County" dialect; and four modified varieties of this last. The shadings have not been done in a haphazard fashion, or by guesswork; but painstakingly, and with the trustworthy guidance and support of personal familiarity with these several forms of speech.
I make this explanation for the reason that without it many readers would suppose that all these characters were trying to talk alike and not succeeding.
Aunt Polly uses the Pike County dialect as does Tom, Huck, and Pap. Among the features of this dialect are the deletion of initial unstressed syllables and the accentuation of stressed vowel sounds. Examples of the former occur in Pap's 'lection (election) and Huck's 'deed (indeed). As for the latter, Aunt Polly says owdacious (audacious), creating an exaggerated diphthong of the first syllable. She does something similar with clothes and clo'es, and here Twain accentuates the diphthong in her speech with an apostrophe and the deletion of the "th". The resultant sound of the Pike County dialect is a twangy, drawling thing.
With regards to "Y-o-u-u Tom!" my conjecture is that she is obeying both of the above rules. She is deleting the unstressed syllable--in this case, a whole word: "Hey"--and she is accentuating the stressed vowel, possibly making it a diphthong owing to the second "u" in "Y-o-u-u Tom!". In short,
"Hey you, Tom!"
(I doubt any connection to yoo-hoo, which, as has been discussed in this and this EL&U post, has more to do with the "pirate" expression yo-ho than it does with you.)
For an interesting discussion of the accuracy of Twain's claim that only seven spoken dialects occur in Huck Finn, this article by David Carkeet is a good read.