Short answer: no, if properly controlled.
What you described was poor, perhaps linear control of a loud fan. Using good control with efficient coolers and silent fans will make sure the transitions are not jarring and the sound levels remain sane - or indeed silent.
Long answer: No, and here's why.
I have always loved and used manual fan control since the day I discovered PC silencing in 2004 or so. The automatic fan control in those days either sucked hard or did not exist, the first still being true of (cheaper) systems today. When you know what you are doing, you can easily avoid fan zig-zagging and excessive volume levels
. Software like Speedfan and most recently Asus' Fan Xpert+ and Fan Xpert 2 can be used for this, as can some smarter hardware controllers, but the controllers are becoming a thing of the past as motherboards get better features. Abit already showed the world that controllers were redundant with their µGuru many moons ago (LGA775 days).
To give you an example, I have the Asus P8Z77M-PRO motherboard with Fan Xpert+ that allows me to set the fan profiles, presented as "curves" (drive/temperature graph), manually. My current setup involves 4 fans: two low-RPM intakes, one static RPM CPU cooler fan and one exhaust. I don't count the PSU as it is silent and non-controllable.
Here's some profiles: http://imgur.com/a/9B4Eu
The first profile is the CPU cooler profile. I use a fan running at a static speed
I find comfortable for cooling the CPU in any situation. This gives me not only unchanging noise, but predictable cooling behaviour
, helping avoid zig-zagging through a controlled change of the temperature reading used as the profiles' "trigger" value.
The second profile is the exhaust fan. It uses a linear profile
, which used to be the most prevalent type in cooling systems of old (and still is in most of the cheapest ones). This gives a direct, immediate response to temperature rise and I prefer it because it's important to exhaust hot air ASAP to prevent heat buildup under load. You can typically use a small motor, high CFM fan for unimpeded exhaust, meaning the response will not be very audible (or in case of my Noctua, noticeable at all) but still effective.
The third and last profile is the intake fans. They use a progressive profile
(well, as progressive as three-point control allows), which means that the fans respond to heat depending on the level rather than the absolute figure: the fans only speed up a little when there's not much heat, but respond more aggressively as buildup or high load occurs. They've also been cut more slack in regards to the trigger level to be reached. I've raised the bottom drive level to emphasise the progressive profile's difference to the linear; I prefer to run at the minimum of 41 % drive (700 RPM for these fans).
The points on the temperature scale were chosen through rigorous testing.
The first trigger point should be above idle and typical load
- in my case this is under 35 °C. This way fans will stay at a steady RPM in normal use, silent fans and efficient coolers having no trouble staying inaudible at these levels.
The second trigger point defines the first stage of controlled cooling (between points 1 and 2) and should be above typical maximum load
- I went with 45 °C in this example, can easily stretch to 50-55 degrees. For this stage I find the maximum comfortable noise level of my fans first (usually under 1000 RPM for 120 mm fans), then set the computer to run a "typical maximum load" task like defragmenting or a virus scan and adjust the fans down until I find a comfortable and stable temperature level. This stage takes the most learning (patience, really) at first as you have to tweak the fans as a system and at varying load. The end result is efficient cooling response to loads over regular use with fans still running at comfortable levels - very nice when the PC is left idle and AV starts, for example. The longer you make this stretch, the smoother (more gradual) the response is.
The last trigger point could be used to make the cooling three-stage, but I don't like making big jumps in fan control for fear of stressing the delicate electronics. This should essentially be the point where you don't want your temperatures getting any higher, and I usually set it just below TCase (in layman's terms, this is a value given for the CPU over which they should not be allowed to heat, even though it will not break the CPU to do so). In this case it's 65 as the i5-3570K has a TCase of 67.4.
This is what I use for a gaming and work PC. If you never game or do anything heavy-duty like that, you could make the profiles even more refined by using the last trigger point to create a smoother stage 2. Then again, in a computer that runs intensive tasks like folding or rendering for long stretches of time, static fan control is a strong candidate, as you can try and find a comfortable level at maximum stress and just leave the PC there - peace of mind with minimum effort.
Sorry if the latter part of the post got a bit long, but this is such rudimentary stuff I felt like shedding light on the basics through example.
Edit(s): double post got what was supposed to be v2.