I just got a RPi3. I would like to use it in enclosed plastic case like my RPi2. I have a heatsink and thick thermal pad lying around, it covers both SoC and the other chip on the front of the board. In order to mount it without risk of physically damaging something, I will have to use parts of thick thermal pad (the one on photo) on SoC, the second chip, display connector and USB casing.
Should I use the heatsink as described, or avoid using it and run the Pi3 without any cooling? Sadly, these are the only alternatives available at the moment - proper heatsink/case will take ages to be delivered. Cooler is definitely out of the question, I need it silent.
Please advise me! I’m eager to use the new board - but not to a point of risking damaging it, of course.
Generally speaking, if unsure, dont risk it 
Although, as long as there is no direct (metal) contact from the heaksink to any components on the board, it should be fine. The last thing you want is to create a circuit from 1 part of the PCB to another, via the heatsink.
The RPi 3 does run hot and it does require a heatsink (in my eyes), however, it is rated to 85’C and thermal throttling will attempt to prevent it going higher than that, although, as most have noticed, the surface heat of the BCM 2837 is around 10’c hotter than the probed temp.
@Fourdee thank you very much for your reply. I believe I will be able to fit it without touching the USB board and plastic of connectors. My main concern is whether it is acceptable to have the BCM chip and the second chip on the front of the board sharing one heatsink, or not.
BCM runs a bit hotter, so it may actually increase the heat of the other chip, so you’ll need to monitor it:
@Fourdee SMSC 9514 has max operating temp limited to 70C. Is there a way to monitor it’s temp using software?
Yep , BCM is on left, other chip (SMSC 9514) is on the right: http://i.stack.imgur.com/C8TaU.jpg
Not as far as i know, doesn’t have a heat probe sensor. cpu temp should give you a ‘rough’ indication due to shared heatsink, but if in doubt, do the burn finger test on heatsink to get a rough idea
