I'm playing with a yeast starter right now and I've noticed when I shake the mix the yeast gets more active. I'm wondering how this applies to my actual fermentation. So I was thinking I'd let my primary sit still for 2 weeks then move it to a secondary carboy and shake it up. What are some best practices here and what can make the yeast perform the best?
EDIT: As far as a best practice, I would SAPS it :D (FYI, I made that acronym up...)
Starter - Create a starter to get the cell count high enough - http://www.howtobrew.com/section1/chapter6-5.html
Aerate - Before pitching, use one of the many available methods to aerate the wort - http://www.howtobrew.com/section1/chapter6-9-2.html
Pitch - When the starter is ready and the wort is aerated, put the yeast into the wort in the primary vessel - http://www.howtobrew.com/section1/chapter6-6.html
Suffocate - Do anything possible not to introduce oxygen after this point - http://www.howtobrew.com/section1/chapter6-9-3.html
It is not recommended to perturb the beer between when fermentation starts and kegging/bottling because you run a strong risk of coming into too much contact with oxygen. Carefully racking to secondary with minimal oxygen exposure will leave you with plenty of yeast for carbonation.
Please see Why do you aerate wort at first and try to keep oxygen out later? for why oxygen is not good for wort/beer once fermentation has begun.
Your yeast is not getting more active its just bubbles. Shaking the completely fermented beer is only knocking CO2 out of solution. Shaking in secondary can be a problem if there is O2 in there. It will mix with the beer and likely cause some oxidation.
...so you want to shake the yeast after fermentation is complete and you've racked off the lees?
If anyone disagrees here, please weigh in, but I don't think you'll see a difference, and if anything, you're at a slight risk of oxidizing your beer.
If you're talking about how the Wyeast pack balloons up after you shake it, that's because you're knocking a significant volume of CO2 out of solution, causing the bag to expand.
If that's not what you mean by "gets more active," please elaborate. Whatever you're observing, though, is likely just foaming of CO2 from agitation, rather than an actual change in yeast metabolism rate.
In any case, there is some merit to rousing yeast and helping them attenuate a beer, particularly if it's a highly flocculent strain, as they tend to settle out before they can fully reabsorb the diacetyl and acetolactate. This, however, is more effective if you do it at the end of primary fermentation, not a week afterwards. You can achieve the same effect by raising the beer to a diacetyl rest temperature at the end of fermentation, typically about 5°F warmer than your fermentation temperature.
Another downside to shaking after fermentation has begun is you run the risk of getting the dried Krausen off the side of the fermentation vessel. That mixed with the extra oxidation you'd cause can cause quite a bit of bitter, papery off flavors.
Shake it up, but only after the aggressive fermentation period is over with. This will typically be 4-7 days in the primary. Only shake in the primary! You risk oxidation at any other point. The oxygen has already been forced out of the carboy, shaking can in fact liven the yeast and make nutrients that settled into odd areas once again available to them. I recommend shaking during week 2 and beyond. Obviously if you are near bottling time, you want to leave amply time for settling (minimum 3 days).
I am an avid from-scratch brewer and base the above off of both my own and other's experience, in addition to a little common sense applied to the science behind the brew.
From commenter Mike S: http://www.howtobrew.com/section1/chapter6-9-2.html Explains why you shake at the beginning. http://www.howtobrew.com/section1/chapter6-9-3.html Explains why you do not shake after primary.