With a lot of 50mm carbon deep v options popping up (November, Boyd, Williams) for around $1000, how much better is something like a Zipp 404 or Bontrager Aeolus 5.

Are these wheels worth double the cost of their less aero competitors?

I have both currently and can tell you that there is a minor difference, whether or not it is worth the money is up to you. In my opinion, it is not. Unless of course that minor difference will make you money or fulfill you in some other way. I have actually found that while my Zipps are slightly faster once up to speed my Reynolds DV46c UL's accelerate so much faster I prefer the Reynolds. On top of that the Zipps have been noisy, don't maintain spoke tension as well and flex more.
In the end, there are better ways to spend an extra $1500 or so.

I need new wheels, but these noise and flex issues keep coming up. Just when I think I'm ready to make a purchase.

I way prefer a quiet and strong bike, even at the risk of, dare I say, increased weight.

Get a pair of Shimano C50 wheels then? Quiet, smooth hubs, hardy rims and pretty stiff it seems. Just that the clincher versions are somewhat porky.

i have c50 tubulars and i can't see any reason i would ever switch from them. even though they are ~1500g for the set, i think that the quality and durability more than makes up for it.

i'm an 83kg sprinter/tter and they feel rock solid when i put down power, love them.

I've owned multiple sets of the firecrest 404's as well as the reynolds in both the standard assaults and DV46's. Current stable includes assaults and 404 firecrests.

Every one of the afore mentioned wheels have broken a spoke on me. The reynolds a couple of times, the zipps only once, and it was not a spoke. The head of the nipple actually broke. Zipp took care of it with no problems.

A few friends of mine have had on average 2-3 spoke breakages on the reynolds. Each time, reynolds stood behind the wheels and replaced the spokes and trued. No issues at all.

To the poster who says that he claims that the DV's accelerate much faster than the zipps, I would argue that for me, there is no noticeable difference in acceleration between the 404FC or any of the 46mm reynolds I own, the exception being the DV32T's I have, at almost 500g lighter, then it's not so much the acceleration rather the general ride quality and feel between them. Based on sheer mass, I think you would have a difficult time quantifying/measuring any differences in acceleration between the 404FC and the 46's. I don't feel any difference in that regard though zipps wind tunnel data, along with my impressions, suggest that they might carry speed a bit better.
I find that the 404's are quite stiff in the vertical plane compared to the reynolds. I weigh 160ish.

Where there is no comparison between the 46mm reynolds and the 404FC is in crosswinds. The zipps are magnitudes better in crosswinds. The reynolds feel in strong winds as if someone has grabbed your bars and yanked sideways on them whereas when riding the zipps in similar conditions on the exact same stretch of road, it feels like someone is just pushing on your hip a bit, much easier to handle. The difference is huge in that regard. In many situations, it just means you have to take a bit more care and allow for run off side to side to allow for corrections in your line.

It could also mean that you might have as much as 10-15 bike lengths lead on your buddy/others on the ride/race if they were hypothetically using the reynolds or similar wheel versus you being on a 404FC on a windy descent. When the response to side gusts are much more linear, as the zipps appear to be, you don't need to allow for as much runout on the road on each side to counteract forces pushing you sideways, and in many situations, I don't even touch the brakes whereas I've needed to slow down on other brands for fear of getting blown sideways and running out of road or getting blown into the other lane on a 40+ mph descent.

The braking surface and consequent braking performance, in my opinion, has been equal between the zipps and reynolds. They both stop well.
Are the differences worth $1000? Only you can decide that one.

I have used Zipp 404s (pre-firecrest), Reynolds and Gigantex wheels. In my experience, the Zipps handled much better, especially in the wind. For me, when I buy another set of carbon wheels, I will spend the extra money and get ones that I think I will get the most use out of because of my perception of stability, so it will be either Zipp Firecrests or Enve Smart System unless someone else has something similar out by the time I'm ready to drop the money. While someone else can post data on this, I recall seeing numerous places where the Zipps are faster than the other wheels mentioned by the OP.

at only 130#'s sound like I'd probably benefit from the newer wheels designs.