It would probably be best to give each voter a "yes" and "no" address that they are expected not to share with anybody else. They can then vote by sending the right number of bitcoins to one of those addresses.
You can decide what happens if they send to both addresses.
If you want the vote results to be public, then you can pre-publish before the vote a hash of the list of all addresses and voters. Then after the vote publish the list; everybody can make sure it hashes to the correct value, that it has the right list of voters, that it has twice as many addresses as voters, and each voter can check to make sure the addresses assigned to them are on the list.
And the voters could then look at the transactions in the blockchain during the voting period, to those addresses to audit the vote.
There's probably a complicated crypto protocol you could put on top to make the votes anonymous-but-verifiable, too -- so even the vote organizer doesn't know who voted for what.
Ok, I was looking at having a list of voter addresses that would then send to either address 1Yes1lksd8sdf986ad5ffasd57a9 or 1No1dfs6as5f4asd3a4h587dfa. Before the vote, everyone would know how many voters there are, a list of all of the addresses, and you could verify that your address is on the list.
Then when it is time to vote you combine your wallet into a single address and send a mBTC or whichever to the address you support.
At that point, everyone can watch the tally as it comes through, they can verify that the right addresses are sending to the final addresses. Any address not in the list would be refunded. And any amount above the agreed upon vote amount would be refunded. The address with the most BTC wins.
I was trying to avoid the use of individual addresses because I did not want the man in the middle being able to play any role once the stage has been set for voting. I can see how pre-publishing a hash of the list could work, while also having the added benefit of not having a final result until after the vote is over as to not influence those who have not yet voted.