OK, I am a big, big fan of racking out of the primary fermenter - whatever you are using - and racking into a secondary (airtight) fermenter. Secondary fermenters should be either five-gallon glass carboys or five-gallon Better Bottles. That's it. If you are not going to rack into either of these, just go ahead and bottle without any secondary aging. Your product will be better, and less likely to oxidize and spoil. Stagnant aging of fully fermented beer or wine cannot successfully be done in regular plastic five-gallon "water bottles", dig? They are not oxygen-barriered.
OK, here is the scoop on this misunderstood process.
The nearly-finished-fermenting liquid should remain in the primary fermenter until the fermentation is almost completely done. You want 95% of your fermentation to be completed in primary even more if you are doing a lager. DO NOT RACK AFTER "X" AMOUNT OF RANDOM TIME, no matter what your recipe says. Think of your fermenters like children, some start walking and talking sooner than others, usually there is no problem with these variations, it's just the way Things Are. Therefore, do not expect every beer or wine you brew to be racked after three, or five, or seven days, irregardless. Each one is different. Watch them and accept them for what they are.
For ales, when the airlock drops its activity level to about one bubble every 90 second interval - that's one "bloop" every minute and a half, it is ready to rack to secondary. For lagers: wait until every three minutes between bubbles. That can be one week, two weeks or more. Most ales fermented with liquid yeasts will be done in 10 to 18 days; an ale fermented with dried yeast will typically be finished and ready to rack in 1 to 4 days. Lagers may take three or more weeks to reach this slow level of activity.
Why wait until this time? The beer fermentation is kept active by sitting on the sediment - this is a good thing. The yeast "use" the sediment as a nutrient source, and the fermentation stays healthy and active. Once you rack off, you risk stunting the fermentation and leaving the beer residually sweet. Also: the yeast reduce this certain buttery essence - called diacetyl - at the tail-end of the fermentation. Racking too early can leave behind this "artificial butter" essence ad nauseum in the flavor profile. On the other hand, you want "some" activity to occur in the glass secondary in order to produce carbon dioxide to flush out the oxygen sitting on top of the liquid. If you wait too long to rack, your beer or wine will no longer be producing carbon dioxide and the beer in the secondary will have a layer of bad oxygen resting on top of it while it ages.
For wine, if you plan on trying to leave some residual sugars (mostly sweet whites and fruit wines), rack early: when the hydrometer is reading about 3 to 5 Brix. For dry white wines, and most red wines, rack out of the primary when the hydrometer is reading 0 Brix, or even a little lower (negative 1 Brix). But do not let the wine sit in the primary after that point, unless you are very experienced and doing specialty fermentations
The reason you do not want to let your finished product sit in the primary too long is that once the beer or wine fermentation is done, the yeast (still wanting to remain alive) will start breaking down the dead sediment (autolyzing it)in a sort of survival mechanism; this can give the beer or wine a rubbery "yeasty" flavor. This is the cause of most "yeasty" flavors in beer, not actual yeast floating in suspension. So you must rack out of the primary fermenter no later than the end of the fermentation.
So when the fermentation slows way down - remember the guidelines above - you are ready to rack to secondary. A glass secondary (or Better Bottle) will keep oxygen from getting near the alcohol molecules - oxygen is VERY bad! (For wine, it is the worst danger you have, bar nothing.)
The process of racking (siphoning) is fairly straightforward, especially if you have the right tools. All of our starter kits have "auto-syphons" in them. This makes the process foolproof. Remember, when siphoning, gravity is your friend. The bigger the height (gravity) differential between the liquid-filled container, and the empty (receiving) container, the easier your liquid will flow. The filled container should be on a countertop, the empty container should be on the floor. You should have at least five to six feet of flexible siphon tubing hooked onto your auto-syphon. If you have less, think twice about siphoning: you will splash and oxidize your product. Many stores sell their customers three feet of siphon tubing this is ridiculous, and you cannot successfully siphon with this small length. Ask for you money back. You need five feet minimum. Main Street usually sells six-foot lengths, just to be sure.
Place the lower end of your siphon tube into the BOTTOM of the receiving (empty) container. Hook the other end to your sterilized auto-syphon. Hold your auto-siphon in the middle of your liquid-filled container. DO NOT rest the auto-siphon in the sediment on the bottom of the fermenter. Pump your auto-siphon a few times, and the liquid should begin to flow into the bottom of the receiving container. As the liquid drops out of the filled container, move the bottom of your auto-siphon lower to keep it submerged. Eventually, you can tilt the draining container into a 45-degree angle, and suck the pooled liquid off of the "pancake batter" sludge that covers the bottom. If you happen to vacuum up some of the sediment, do not worry - it will settle out in the secondary. That's it.
Allow the racked beer to sit quiet and dark for one to two weeks. This will allow the stragglers to settle out - now there are not enough yeast cells to autolyze - and the flavors will clean up and "round out" with the bulk aging. If you are making beer, after one to two weeks in secondary, you are ready to bottle.
For wine, wait four weeks, then rack into another (smaller) glass fermenter. being sure to keep the wine topped off in the neck of the new carboy.
Under no circumstance should you strain or filter the beer or wine as you move it from primary to secondary, or anytime that you rack - this will cause massive oxidation. Leave the Forces of Gravity to do their job and all will settle out with time. Also, when racking, make sure the "spitting-out" end of the siphon tube is placed into the very bottom of the receiving carboy - this will also keep oxidation from occurring.
E-mail me if this is not clear, or if you have any questions that go deeper.