Seen the usual BSO factory-built horror shows (machine made and not QCd) but also seen disasters made by those who know better but couldn't be arsed (and I know they know). Also had more than a few pairs of 'value' but not cheap wheels from large UK distros that needed more work than was reasonable to be fit for use. At the end of the day though, everything should go through a stand before it meets a bike as even though it may look good, tensions can be all over the place and it'll come back quickly.
If you're suitably competent (or willing to learn, eg. via Musgrove's book or a class) and the cost of yours or someone else's time isn't a factor then hand-built means you'll get what you want. You'll know the spokes have been correctly set, are the correct length and with sufficient engagement with (appropriately treated) nipples, and that tensions are sensibly balanced.
In realty though, unless you're buying in bulk the price of hub, hoop, spokes and nipples quickly overtakes the cost of mid-range factory built wheels, and that's before you consider the cost of a builder's time. If you're price sensitive then you can get some reasonable quality wheels for sensible money and just resign yourself to giving them a once over before use. That said, if you're happy to pay, there are some extremely competent UK wheel builders that offer some actually very fairly priced 'stock' builds.
As for decent factory-built, I recently ordered a pair of rim brake hybrid wheels from Madison (decently made eyeleted rims, Shimano C&C hubs, plain spokes) and they were spot on; good solid workhorse wheels that should last until the rims go, for less than I could've put them together. The only issue was the hub logo not facing the valve, but I can live with that and the customer wouldn't have noticed if I hadn't pointed it out.
Short answer: 'it depends'.
