How about something like this? It doesn't look pretty and I'm sure with enough space and a slim fan it could be done neater, but it's the result that counts. Perhaps one of the options he rejected might work for you.

If using a tower case try installing getting a larger fan on the side of it, that's what I usually do, or using o a PCI fan bracket, while a small fan screwed on top of the heatsink would also work these smaller fans are very prone to malfunctioning and unless you monitor constantly it may stop functioning and go unnoticed for a while.

If there is enough room between the top of the boards and the case, then you might be able to fit a fan that draws up air from between the boards.

Thanks! Something like below? Not exactly cheap for this purpose and also wondering whether this would even give enough cooling as it wouldn't be applied directly to the heatsink?

 

https://www.amazon.com/GeLid-SL-PCI-02-Slot-120mm-Cooler/dp/B00OXHOQVU/ref=sr_1_9?ie=UTF8&qid=1524395073&sr=8-9&keywords=pci+fan+bracket

That's a very high-end route.

 

If you can figure out somewhere to fasten the fan, you could consider something like below, with a standard - and rather low-speed - fan:

   ^   ^   ^
+--------------+
|  ^  FAN  ^   |
+--------------+
 |   |   |   |
 | ^ | ^ | ^ |
 |   |   |   |
 | ^ | ^ | ^ |
 |   |   |   |
----------------------------- Motherboard

 

Agree that this is high-end and I'd very much prefer not to spend the money. Even more so as I have some doubts that even the high-end route will provide sufficient cooling.

 

I also don't like the path of having a fan somehow screwed to the heatsink as it indeed looks ugly. Plus I hear your point that these fans are keen to failure and I may not be aware (plus cumbersome to change in the future).

 

Your drawing is very helpful. I have enough space to go this path, but I am not sure how I can fixate the fan. Saw some notes about magnetic ways to fix it. I am not sure whether my tower allows this. And this would not be better (and only somewhat cheaper) compared to the "high-end" way?

I have made use of the screws that holds down individual cards to fixate two corners of a fan placed above multiple boards. The fan frame itself rested on the boards.

 

So my cost was the cost of a single chassi fan and a bit of own time.

 

If the case has a metal side, then you can also cut out a hole in the side of the case and mount the fan - but then you need to find some wire mesh or similar on the outside so you don't risk putting your fingers into the spinning fan.

These are hard to find now but I've used these for my PCI cards.

https://www.newegg.com/Product/Product.aspx?Item=N82E16835118204