It is generally recommended that supported Unified Communications Certificate Partner public CA is used for all public certificates Lync Server 2013:
Unified Communications Certificate Partners
Also if your running Lync Phone Edition you should be mindful of the public trusted certificates installed by default:
Certificates for Lync Phone Edition
A number of certificate providers are transitioning to the SHA-2 cryptographic hash functions which allow greater levels of encryption. I experienced this recently with a GoDaddy certificate reissue (whereby I needed to change the existing certificate) this causing federation issues with some organisations but not others as the new root certificate wasn’t as widely installed as Edge server are typically on restricted networks and thus might not be getting the root certificate update from Microsoft.
This came into effect with Go Daddy 23 December 2013 and is why there is now a new root certificates (‘Go Daddy Class 2 Certification Authority Root Certificate – G2’). It is possible (at the moment) via changing the ‘signature algorithm’ during the CSR submission to still do a 2 year certificate using the older root certificate and chain. (See below)
What I will say however Microsoft themselves as well as Office 365 use Cybertrust
So does it matter? Well as long as the computer/device trusted the certificate it should not, although I like others have had certificates issued with previously OCS/Lync deployment from both the UCC partners or other providers not listed.
And Lync is all about certificates…………….
Information About Requiring the SHA-2 Hash Function’ may be helpful to you.