The best I've ever used? Easy.
MainConcept Reference 1.6.
MainConcept 2.x was excellent as well, but far more confusing to use. And sometimes I saw oddities in the encoding of both H.264 and MPEG-2. I wasn't fond of it.
Adobe Media Encoder (AME) was based on the MainConcept SDK. AME has a custom front-end, but MC powered it. Sony uses it as well for Vegas.
I forget the exact year, but MainConcept was then sold to Rovi, which also owned DivX. Reference was renamed to Rovi TotalCode, though the SDK is still called MainConcept. Nothing really changed on it from MC 2.0 aside from the name.
The company was German, but is now mainly Russian. No idea what happened to the MC encoding team.
Last year, Rovi sold off the encoders to
venture vulture capitalists:
http://www.rovicorp.com/company/pres...usinesses.html
No idea what will happen to it now.