Yosemite bluetooth audio is choppy/skips
It's an issue with the amount of power/bandwidth supplied to the BluetoothAudioAgent, the daemon in charge of streaming. Apparently most people have had success by entering the following command in terminal.app: 

defaults write com.apple.BluetoothAudioAgent "Apple Bitpool Min (editable)" -int 40

Source: http://lifehacker.com/fix-your-bluetooth-audio-in-yosemite-with-this-terminal-1670380974

The source article lists Yosemite as the specific OS this applies to, but I know that this fix also works back to Mavericks and (possibly) Snow Leopard (untested).

I am having this exact issue at the moment and entered that command with non-noticeable results. I'm going to reboot the machine and see if that takes the new settings into account. But it seems like this command is the way that the wide majority of people have resolved this issue. 

EDIT: Just rebooted, the audio quality is significantly better. No noticeable choppiness whatsoever (knock on wood). It appears that the command I posted above does seem to resolve the issue. 

EDIT 2 (2015-8-24): The above command does help in many cases and produces noticeable quality improvements. Unfortunately, however, Yosemite is very moody with regard to bluetooth audio. The problem compounds itself when in proximity of other bluetooth devices. To expand on my previous answer above, I highly recommend entering the following additional commands to increase other bluetooth audio parameters:

defaults write com.apple.BluetoothAudioAgent "Apple Bitpool Max (editable)" 80 
defaults write com.apple.BluetoothAudioAgent "Apple Bitpool Min (editable)" 48 
defaults write com.apple.BluetoothAudioAgent "Apple Initial Bitpool (editable)" 40 
defaults write com.apple.BluetoothAudioAgent "Apple Initial Bitpool Min (editable)" 40 
defaults write com.apple.BluetoothAudioAgent "Negotiated Bitpool" 58 
defaults write com.apple.BluetoothAudioAgent "Negotiated Bitpool Max" 58 
defaults write com.apple.BluetoothAudioAgent "Negotiated Bitpool Min" 48


EDIT 3 (2015-9-08): Alright. I'm sorry I keep updating this answer, but I keep finding more information about this issue (since improving bluetooth audio on Yosemite is a long-term effort, apparently). I've found several sources that cut straight to the mustard and set everything to 80 which appears to be the maximum allowable value for Bitpool settings. If the above settings don't work well enough for you, try the "All In&trade;" approach.

defaults write com.apple.BluetoothAudioAgent "Apple Bitpool Max (editable)" 80 
defaults write com.apple.BluetoothAudioAgent "Apple Bitpool Min (editable)" 80 
defaults write com.apple.BluetoothAudioAgent "Apple Initial Bitpool (editable)" 80 
defaults write com.apple.BluetoothAudioAgent "Apple Initial Bitpool Min (editable)" 80 
defaults write com.apple.BluetoothAudioAgent "Negotiated Bitpool" 80 
defaults write com.apple.BluetoothAudioAgent "Negotiated Bitpool Max" 80 
defaults write com.apple.BluetoothAudioAgent "Negotiated Bitpool Min" 80


To see your current defaults:

defaults read com.apple.BluetoothAudioAgent


Edit 4 (2016-07-14): One more (hopefully last) edit. Make sure that you restart the bluetoothaudiod (or coreaudiod) service after making changes to these settings. 

sudo killall bluetoothaudiod


Or, if you are on El Capitan:

sudo killall coreaudiod


Credit for this goes to the multiple wise nerds below who suggested it. (Thank you!)