After considering the existing answers and doing some additional research, here's my take: Spray-on waterproofing Spray on waterproofing should be used on Multi layer garments.
You only want to treat the outer layer which reduces the chance that it will be 'wetting out' quickly, which allows the inner membrane to maintain it's porous properties.
I've found many references for gore-tex which state "
We do not recommend wash-in treatments, as they can hinder your garment’s breathability.
"
Wash-
In waterproofing Ideal for Single Layer waterproof or water resistant DWR fabrics.
Probably great for your tent's rainfly, cheap rain shell pants, or your single layer packable windbreaker.
Not so good for your multi-layer gore-tex jacket.
Though, you could probably use the spray-on coating for these type of materials as well with little difference in final result.
So, if in doubt, I'd use the spray-on.
Either way, you should keep your garments clean to ensure that body oils and sweat deposits don't clog the pores in the breathable membranes.
Most breathable garments recommend using a detergent free tech wash that won't wash away the DWR treatment.
outdoors.stackexchange.com/users/429/Benzo
Contrary to what a lot of people are saying, the wash-in treatment won't block pores of multi-layer fabrics (unless it's really dirty).The chemicals used are designed to break down particulates as small as possible.
The 'wash-in' also doesn't do a whole lot of actual waterproofing on the fabric, since it's soaked in water itself.
It simply removes dirt and helps the fabric to do its job better.
Your jacket will even look like it's been soaked through (because it has!)
after being washed.
Tumble drying on a low heat will re-activate the garment by expanding the fabric, and making the pores 'smaller' and more one way.
Obviously if the fabric isn't clean, it's not going to do as much, since the pores are blocked.
The spray on is a totally different bunch of chemicals, and would block pores!
It is essentially a water repellent.
This is best applied to a dry jacket and spread around with a small cloth or sponge (note that this material will also become water repellent), and left to dry or tumble dried on low heat.
Extra should be applied to high wear-and-tear areas, such as the shoulders, neck and cuffs.
This lay will be rubbed off over time, and should be applied about 3-5 times in between washes.
-Source:
Worked at a company making such stuff.
outdoors.stackexchange.com/users/7903/Greg
I have garments, such as pertex, with a pile (Buffalo Mountain Shirt) or microfleece lining
(Rab Vapour Rise Jacket).
It's useful to have a DWR treatment on the Pertex to help with water resistance where the lining still needs to cope with excess moisture.
In these sorts of garments you definitely want a spray-on treatment otherwise the action of the lining allowing it to move excess moisture away from skin or base clothing will be compromised if they also become hydrophobic due to the DWR.
For clothing with no such lining where you ant all the garment to be water resistant (or waterproof), then the wash-in sort of DWR, is more convenient and probably does the job better, too.
outdoors.stackexchange.com/users/3061/Paul Lydon
To emphasize what Liam and Paul hinted at, in all likelihood, too much nikwax wash-in and the like could potentially act against gore-tex by blocking the pores and preventing the fabric from breathing ( thus soaking in your own sweat ).
What gore-tex primarily recommends on their site and what I've had more success with is simply tumble drying the garment for 20 minutes to reactivate the DWR every once in a while.
Every so often, I also coat the seams in otter wax to really seal the deal.
outdoors.stackexchange.com/users/1975/Scott Hillson
From the Nikwax website: Wash-In "For the convenience of a wash-in product try: TX.Direct
® Wash
-In " Spray-On "For non-machine washable items or those with wicking linings use: TX.Direct
® Spray-On "
outdoors.stackexchange.com/users/3078/alphaleonis
There are both spray-on and wash-in products available for treating my DWR ( Durable Water Repellent ), gore-tex, eVent and other garments using products such as nikwax wash-in or nikwax tx-direct.  What types of garments is it more appropriate to use spray-on versus wash-in on and vice versa?
When should I use spray-on versus wash-in waterproofer for treating DWR garments?
outdoors.stackexchange.com
<gear-care><waterproofing>
outdoors.stackexchange.com/questions/5432
outdoors.stackexchange.com/users/429/Benzo
Spray on waterproofing should be used on multi-layer garments. For clothing with no lining where you want the garment to be water resistant, then the wash-in sort of DWR, is more convenient and probably does the job better, too. Gore-Tex recommends  on their site is simply tumble drying the garment for 20 minutes to reactivate the DWR every once in a while. However, it is said that contrary to what some people say, the wash-in treatment won't block pores of multi-layer fabrics. The chemicals used are designed to break down particulates as small as possible. DWR treatment is important for water resistance, spray-on treatments and tumble drying are also important.
DWR treatment is important for water resistance. Spray-on treatments and tumble drying are effective.