Most naive approaches to the problem have some serious issues. The worst is how bash.org and qdb.us displays quotes - users can vote a quote up (+1) or down (-1), and the list of best quotes is sorted by the total net score. This suffers from a horrible time bias - older quotes have accumulated huge numbers of positive votes via simple longevity even if they're only marginally humorous. This algorithm might make sense if jokes got funnier as they got older but - trust me - they don't.
There are various attempts to fix this - looking at the number of positive votes per time period, weighting more recent votes, implementing a decay system for older votes, calculating the ratio of positive to negative votes, etc. Most suffer from other flaws.
The best solution - I think - is the one that the websites The Funniest The Cutest, The Fairest, and Best Thing use - a modified Condorcet voting system:
The system gives each one a number based on, out of the things that it has faced, what percentage of them it usually beats. So each one gets the percentage score NumberOfThingsIBeat / (NumberOfThingsIBeat + NumberOfThingsThatBeatMe). Also, things are barred from the top list until they've been compared to a reasonable percentage of the set.
If there's a Condorcet winner in the set, this method will find it. Since that's unlikely, given the statistical nature, it finds the one that's the "closest" to being a Condorcet winner.
For more information on implementing such systems the Wikipedia page on Ranked Pairs should be helpful.
The algorithm requires people to compare two objects (your Pick-A-or-B option), but frankly, that's a good thing. I believe it's very well accepted in decision theory that humans are vastly better at comparing two objects than they are at abstract ranking. Millions of years of evolution make us good at picking the best apple off the tree, but terrible at deciding how closely the apple we picked hews to the true Platonic Form of appleness. (This is, by the way, why the Analytic Hierarchy Process is so nifty...but that's getting a bit off topic.)
One final point to make is that SO uses an algorithm to find the best answers which is very similar to bash.org's algorithm to find the best quote. It works well here, but fails terribly there - in large part because an old, highly rated, but now outdated answer here is likely to be edited. bash.org doesn't allow editing, and it's not clear how you'd even go about editing decade-old jokes about now-dated internet memes even if you could... In any case, my point is that the right algorithm usually depends on the details of your problem. :-)