On a personal note - I've only been riding a few (4-5?) years and only recently (last 24 months or so) have I taken wheels a little more seriously after I encountered some problems with some machine built wheels.
My Giant Defy 1 2015 came with what I am assuming are
Giant machine built wheels branded as 'P-R2'. After around 800 miles a couple of my spokes had noticeably slackened enough that my rear wheel developed a noticeable 'click' and buckle. Returning it to the LBS they retensioned/trued them and sent me on my way. Around 150 miles later the rear had developed the same problem, I investigated how to remove wheel buckles and 'solved' the problem myself. I added tension to much of the other spokes to try and alleviate the problem in future as in comparison to another (cheap Carrera) bike I had (which never had any buckles) they didn't seem very tight. In doing so I rounded several of the nipples with a cheap spoke key. At this point I had probably spent 10-20 hours of toying around, truing and retensioning/balancing these Giant wheels. As I commute by bicycle a deal on some Campagnolo Khamsin came up online and multiple people in the road cycling thread had recommended them. I bought a set and considered the ~£120 investment a saving of the time I had spent on the Giant wheels that I wouldn't need to spend again.
As time went on and I clocked up over 1000 miles on the Khamin's with no issues. They were noticeably smoother and felt more responsive than the Giants, I'm guessing much stiffer rims as the two wheelsets were comparable weights. I became very interested in wheels and invested some funds in the
Park Tool spoke tension meter and along with some ebay bought replacement nipples I replaced around 30% of the nipples on my Giant wheels. I used the rear wheel on my Turbo trainer and upon checking it a few weeks afterward I noted a few had lost a little tension. In retensioning the spokes I noted the replaced nipples hardly needed any work. I replaced all the nipples with the ebay ones I'd bought and although the wheel hasn't done more than a few hundred miles on the turbo it has remained true.
My Khamsin wheels have done 3500 miles and only needed a couple of minor buckles removing. They've had replacement bearings as they have dealt with some pretty horrific winter conditions, this wasn't cheap (£40 at my LBS!) so it is something I will do myself in future after I picked up a bearing press in an online deal. I only recently (last week) 'retired' the Khamsin to winter duties after a pair of Shimano RS81 24's were snagged on a pretty unbeatable deal (£512 down to £360, being sold at £260).
As a carbon/alloy combination they are incredibly light (1500g) compared to the Giants or Khamsins (2kg+) and I've noticed quite a difference when riding, their pickup speed is incredible. As for rough roads and carbon absorbing shocks I've noticed only minor difference. Minor enough for it to be no more than a placebo effect of 'new wheels'.
I'm guessing all the wheelsets I've experience with are factory/machine built. I would say that factory built wheels by Giant are useless. For the wheels on a ~£900 RRP bike to be so bad (that a replacement cheap ~£120 Campagnolo set being so vastly superior) they must be made with very cheap components (nipples) which do not hold tension when ridden hard. I would happily own/buy another Campagnolo wheelset (and would probably have bought some Zondas if I didn't come across the deal on the RS81's).
My next step (under way) is doing a complete manual wheel rebuild. I have bought some second hand parts (Roval deep carbon rims) which I will need to change some hubs on (bearings are old and axle/freehub is 10 speed, I need 11). I have a dishing tool but do not have a truing stand, I'll probably pick one up when I get the hubs (still not decided what I want, probably DT Swiss 350's).
In my opinion for 'cheap' wheelsets (<£150) you cannot go wrong with factory/machine built, providing they are from certain manufacturers in my experience Shimano, Campagnolo and probably Fulcrum are ok. I feel that handbuilt below this price range you are venturing a little into unknown parts/quality and possibly cutting a corner somewhere which may not appear until later in the wheelsets life. I may of course be wrong, but I would prefer to buy a wheelset from a well known company shifting large numbers of them (with the associated warranties) as the company is less likely to cut a corner and the cost 'savings' come from bulk ordering components. YMMV of course.
Prices over that I'd say it's totally down to the individual. If you have a particular 'special' requirement - low weight/certain hubs/certain lacings/wide rims, then handbuilt certainly gives you more options. I would expect many of the 'premium branded' £500+ wheelsets (not to mention Enve, Mavic, Cosmic Carbs, Zipp, Rovals etc) to be initially machine laced and then tensioned/balanced by hand. Many of these companies will 'build' and any rims/spokes not reaching a certain machine tension will be binned and replaced. A handbuilt wheelset the builder is less likely to bin a rim and more likely to balance any inequalities from manufacture in the build. This might mean you get a problem in future from it...?!
Hope that gives some insight into my experiences. If anything it reinforces many of the opinions in both camps on here. FT's quote sums it up as there's just too many variables:
It's not as simple as one is always worth it over the other
