I'm a big fan of the RAM Quick-Grip line of phone holders.
Regular
The standard size version of the spring-loaded RAM® Quick-Grip™ phone holder provides a secure fit for a variety of phones and other devices. The adjustable side keepers ensure devices like GPS units and Bluetooth speakers within the listed compatible dimensions will also fit in the holder...
www.rammount.com
XL
This version of the spring-loaded RAM® Quick-Grip™ holder provides a secure fit for a variety of large phones and other devices. Included is a set of two nuts and bolts to attach the cradle to any RAM® components that contain the universal AMPS hole pattern, including RAM® diamond ball bases.
www.rammount.com
These mounts are waterproof - meaning the mount won't be affected by wather - but I suspect your question was for a mount that protects a non-waterproof phone inside a waterproof case/enclosure.
Here's an enclosure sold by SW-Motech which attaches to their tankbags using a MOLLE mounting system.
For motorcyclists, the waterproof Smartphone-Drybag is the right navigation and transport solution for cellphones up to 6.5 inches in size.
sw-motech.us
I think the challenge is to simultaneously enclose to protect and to feed power to the device (if that's important to you). A properly designed system can do both using either a proprietary connector (eg. RAM's Intelliskin products) or a wireless charger with a compatible phone, where the phone resides in the waterproof case and the mount incorporates a wireless charging base. RAM has offerings in both of those areas.
I personally attach my Samsung phone to my ST1300 using a RAM Quick-Grip XL with a RAM ball on MCL bar riser hardware. The charging system is not waterproof - I use an SAE cable to an SAE to USB high output charger to power the phone. In the event the weather turns liquid, the phone will go inside my riding suit or my tankbag and the weather/dust covers go over the USB charger. It works for me.