It's actually really really complex, and ultimately comes down to a matter of what you believe.
There are two philosophies on that subject, and I am going to give you both sides of the argument to help you understand how complex it really is. There are even too different articles on here one by me and one by Boerderij, and we usually end up posting one after the other. But I thought I'd save us both the hassle and condense them to this single post.
And both takes have sources that we draw from to back up our arguments.
Revvy's take on where "Secondary Fermentation" happens.
Here is my friend Boerderij_Kabouter (or Donkey sniffer's) counter discourse.
http://blogs.homebrewtalk.com/Boerderij_Kabouter/Secondary_fermentation_and_why_it_makes_me_crazy/
Donkey sniffer and I have the highest regards for each other (so much that he lets me call him donkey sniffer since I still can't spell his name ), and both acknowledge that there are more than one way to skin a cat...And actually there's a point where both our takes intersect each other.
But he cites New lager brewing by Noonan, and that is where his view comes from. I think that even though it was revised waaay back in 2003 that it still was written originally much earlier, and STILL represents a time when yeast contact was feared (back in the days when people still believed, perhaps rightly so, in the dreaded autolysis which many of us believe is no longer an issue for homebrewers.) So since it came from a time where yeast contact was not encouraged, and that perhaps it skews towards that idea too heavily.
Texlaw put it into perspective nicely;
...racking during active fermentation is something we did back in the days when homebrewers' yeast was of questionable quality. That just isn't the case, anymore. For that reason, many homebrewers do not even employ a secondary (at least, that is the current trend).
TL
This is an ever evolving hobby, and information and ideas change. And now with places like this with a huuge amount of dedicated and serious brewers, as well as all the podcasts online, you will find the most state of the art brewing info.
There's been a big shift in brewing consciousness in the last few years where many of us believe that yeast is a good thing, and besides just fermenting the beer, that they are fastidious creatures who go back and clean up any by products created by themselves during fermentation, which may lead to off flavors.
Rather than the yeast being the cause of off flavors, it is now looked at by many of us, that they will if left alone actually remove those off flavors, and make for clearer and cleaner tasting beers.
BUT I believe though that Ales and Lager have different requirements and needs. and that Lagers should be treated waaay differently then Ales.....Lagers by nature need to be cleaner, any off flavor is way more evident. In fact most of the "bogeymen" of homebrewers is mis reading things like Palmer's writing about Lagers (like autolysis) and assuming he's talking about ALL beers....
Lagers and Ales are really different animals.. Lagers require much specific techniques....like temp control, d-rests if necessary, etc....And have less margin for error.
If you are lagering you want minimal yeast contact....you want to be within the ball park of completeness of fermentation (whether it's 2/3rds or 100%- depending on whose interpretation) and then you want to get it off the yeast cake ASAP and into the cold for a few months.....That's the point of lagers...they are meant to be stored and conditioned for awhile...so you want to minimize the potential for any off flavors from yeast contact.
In terms of lagers I
agree with him about the reduction of yeast contact, though I stil disagree as to when you move it. I STILL believe like HB_99 said, that you wait til fermentation is complete.
But for ALES many of us no longer even use a secondary, unless we are dry hopping, or adding fruit or oak, or trying to get our beer way from any fruit we may have added in the boil like pumpkin. Instead we opt for a long primary, which renders this argument about secondaries moot anyway.
There's been a shift in the last few years away from fearing the yeast to believing that prolonged yeast contact in primary is good for the beer. It results in clearer and cleaner tasting beer, because the yeast have the opportunity to clean up after themselves. I believe that even John Palmer suggest this in How to Brew.
Leaving an ale beer in the primary fermentor for a total of 2-3 weeks (instead of just the one week most canned kits recommend), will provide time for the conditioning reactions and improve the beer. This extra time will also let more sediment settle out before bottling, resulting in a clearer beer and easier pouring. And, three weeks in the primary fermentor is usually not enough time for off-flavors to occur.
And even Donkey sniffer has suggested that the new brewer try both methods and see what works for them.
It really ultimately comes down to what works for you......Try different ways of doing ANYTHING in this hobby and develop your own brewing process....
As you can see it is a difficult issure to answer simply. ANd many people even swear blood oaths against people who believe differently one way or the other. But I think that Boerderij_Kabouter have kind of been able to get away from the "arguments" and the -vs- mentality and present the different takes on this reasonably. And also show where they intersect.
But this is the important takeaway message...
The good news is that whatever method you choose, you will STILL make great beer. That's the amazing thing about this hobby. There is really no RIGHT way of doing things. There are literally dozens of ways to skin the cat here, and all that matter is integrating whatever methodolgy works best for you into YOUR OWN UNIQUE brewing process.
Hope this helps.
