I'm looking to pick up a glass carboy, but I'm not sure which size. I brew in 5 gallon batches (just starting out) and I'm wondering if I should go with the 5 gallon or 6 gallon carboy.
Thoughts? Advantages of one vs another?
You'll need a 6 or 6.5 gallon carboy to provide enough head space during primary fermentation of a 5-gallon batch. If you go smaller, it will be very messy.
Five-gallon carboys are good if you plan on racking to secondary to let the beer condition. During secondary, there will be little to no foam on top ("krausen") so the head space isn't needed. In fact, some HB'ers feel that the smaller headspace is slightly advantageous in minimizing oxidation after racking.
You can actually use 5 gallon glass carboy with a 1-inch blowoff tube for a primary fermenter in a setup called the "Blow-off Method". The wort basically fills up the carboy, and then the krausen blows off. You need to make sure you have a big blow-off tube since you can get a large volume of blowoff (a 5/16" racking tube will quickly plug). A 1-inch tube will fit snugly inside a glass carboy mouth, but you could probably figure something out for a Better Bottle as well (it has a wider mouth). You also will need to make sure you have a large container of sanitizer to put the end of the tube in — I use a 2 gallon bucket instead of my usual 1 liter water bottle for a regular blow-off tube.
Brad Smith has a good description of this method, with pictures: Better Beer with The Burton Union Blow-Off Method.
I've tried it a couple times and it seems to work well, although when I'm using that technique I will tend to lean towards the lower end of the recommended fermentation temperature range to keep the yeast activity from running wild and making a mess. I've never had it overflow, but it's definitely a possibility.
One pro of this method is that you get a lot of the break material and hop bits out of the beer, since they're pushed to the surface and then out the tube. However it's possible that you'll lose a bit of yeast, so I'm not sure if it would be a good technique if you wanted to harvest and wash yeast (haven't tried so I really can't say).