http://www.worldwidewords.org/qa/qa-sha2.htm

"Its recorded history began — at least, so far as the Oxford English Dictionary knows — in the issue of the Lancaster Journal of Pennsylvania dated 5 August 1818: “We have in Lancaster as many Taverns as you can shake a stick at”. Another early example is from Davy Crockett’s Tour to the North and Down East of 1835: “This was a temperance house, and there was nothing to treat a friend that was worth shaking a stick at”. A little later, in A Book of Vagaries by James K Paulding of 1868, this appears: “The roistering barbecue fellow swore he was equal to any man you could shake a stick at”.

The modern use of the phrase always exists as part of the extended and fixed phrase “more ... than you can shake a stick at”, meaning an abundance, plenty. The phrase without the “more than” element is rather older, but not by much.

. . .

The sense in the second and third quotations above seem to fit this idea: “nothing worth shaking a stick at” means nothing of value; “equal to any man you could shake a stick at” means that the speaker is equal to any man of consequence.

Where it comes from can only be conjecture. One possibility that has been put forward is that it derives from the counting of farm animals, which one might do by pointing one’s stick at each in turn. So having more than one can shake one’s stick at, or tally, would imply a great number."