We use Linux, and preferably 64-bit Linux where possible, for everything to do with data acquisition except for Network Attached Storage units which run FreeBSD, though those are basically ``appliances'' which only do a single function, that of serving files over NFS protocol.
For data acquisition, specifically, detector hosts, session hosts, and display hosts currently use Sidious Linux (version 12) which has been assembled in-house. None of the software that has been written relies specifically on anything provided by Sidious Linux other than versions of system packages also available on Debian or CentOS or other distributions, but we get to control them tightly. We also change them very infrequently. This is by design, to provide maximum stability to the environment which must run this software for many, many years - often long beyond the point where other distribution's updates have broken things.
Our MegaCam Detector Hosts run a special version of Linux Kernel called RTAI Realtime Linux. This is a hard (deterministic) real-time operating system which was required to handle the strict requirements of reading out MegaCam's controller. It will be phased out this year (2016) with the roll-out of ``MegaCam FAST'' upgrades. In the past decade-and-a-half, advances in computer hardware and the Linux kernel itself have eliminated the need for a special kernel for this application.