[Rawgrip]

But All I Care About is Hypertrophy?

Also, let's not forget the neural components that have nothing to do with hypertrophy . Hypertrophy over a period is strategically induced microtrauma through progressive loads (i.e. increased workload by raising weight/more work with same weight/combination). And really, you don't get much out of one session so the name of the game is looking at progression over an extended period. Enhanced neural capability leverages your ability to do this and the resulting hypertrophy gains. Better neural = better potential hypertrophy. Don't believe me, think about the much loved "newbie gains" where everything works. What is this phenomenon - muscle is muscle? Well the main driver is rapidly developing neural adaptation and that drives weight on the bar which drives progressive loading which drives hypertrophy. Doh.

So now we know hypertrophy and that neural adaptation is a good thing not some unrelated oddball of nature to be shunned. I'm not saying you need to do a pure powerlifting or peak strength routine and focus on the extreme end of max singles and doubles either - merely that some neural focus is quite helpful and should absolutely be a part of any mid to long-term plan.

Well what's the best way to get a lot of hypertrophy for those looking to add muscle mass? Well, the body is a system and adapts best as a system. This is what makes squats, deads, rows, cleans, presses, and snatches very effective. You are using a large portion of your body's musculature to move a heavy weight (think intensity) through a fundamental range of motion. This is full body lifting stressing a large portion of the body's musculature all at once (microtrauma - especially good to bring up weak links and solidify the body's capability to work well as a single unit - and this is what "functional" is all about anyway). So adding weight to these exercises should net hypertrophy over the entire body. And we all know how hard it is to grow a muscle in isolation and that the body tends to stay within reasonable parameters of balance, just look at the curl boys who otherwise would all have huge arms - the training and workload is there and hitting the target muscle, the body just doesn't adapt like that past a fairly marginal point.

5x5 and Hypertrophy (Stopping Insanity 1)
Also, I keep hearing "5x5 will put muscle on you if you eat enough but it is not a hypertrophy program."
1) No program will put muscle on you if you don't eat enough, come the hell on.
2) As discussed in the Training Primer, hypertrophy is mainly centered around relatively high levels of tension (load on the bar relative to your capacity) and volume of work. 5 sets of 5 reps enable both and strike a good balance (not golden, not directly from God, not the only rep and volume range you'll ever need, not magic - just a good general balance for highly productive core lifts).
3) Load progression (through adding absolute weight/tension, volume/work or a combination yielding more total workload over a period) is fundamental to hypertrophy. One of the things that enables this progression and subsequent hypertrophy is neural adaptation - rapid neural adaptation facilitating progressive loading is what is behind the newbie gains that everyone enjoys early in their training career (so yes, it matters). Sets of 5 are very good at driving the neural adaptation and far better than higher rep ranges (and so is higher frequency which is why you see 2-3x weekly sessions on the same lifts). Combine that with levels of tension and enough workload and you get a very balanced program. Keep in mind, this isn't about maximizing hypertrophy for a single workout. This is about maximizing hypertrophy over a period of time, and the continued neural adaptation allows for more load on the bar and total workload - hence hypertrophy providing your diet is geared to that goal.
4) That doesn't mean that sets of 5 are the end all be all of programming. All that means is that it's a decent foundation, it works well, there are very good reasons why it works, and I'd venture for most people, no matter how advanced or for most specialized purposes, it would be useful for at least part of the year.
5) And just for the record, a complete hypertrophy plan is likely going to require multiple phases to bring one's physique to the pinnacle of achievement - if that is the goal and someone is narrow-minded enough to believe that I'm actually talking about a career or even a yearly plan. Just to be clear - this is the type of work that gets the novice started or helps someone pile on the foundation muscle to move up a weightclass.

This is just of madcows 5x5 website still worth a reading Training Primer

I still think any training needs to work on periodization. Another thing why keeping your training regime the same is not so beneficial because your body adapts
after 4 weeks and you need change (Not to sure now, Mark Rippetoe mentions it on a crossfit interview) Thats why periodization stages work great.