Personally I have integrated both ISDN lines and SIP Trunks with OCS 2007 R2 and Lync 2010.
I have found the best software to use if you want to go down the free route (also unsupported by MS) is to use FreeSWITCH. It can do the bridging between your SIP Trunk on UDP SIP to Lync on TCP SIP (with TLS included if you are that way inclined).
If you want to go down the supported, expensive route, the NET UX2000 is an amazing unit. It can take SIP trunks and ISDN lines. It fully supports Lync 2010 and TLS. It can also do some cool stuff with AD integration.