I use avconv, which is a tool for running stuff through libav. It's free, very fast, and extremely powerful.
My brother prefers MediaCoder, which is basically a Chinese (they have an English version tho) frontend for libav/ffmpeg. It supports OpenCL and CUDA and other nifty things, but I found it to be horribly unreliable.
i7-4790K (Seidon 120XL), 4x8GB DDR3-1866 CL9 1T, GA-Z97MX-GAMING 5, SAPPHIRE TRI-X OC 290X, 128GB Vertex 4 / 4x60GB Vertex Plus R2, SST-DA1000 (PSU), 2x VS229H-P, 1x VG248QE, 1x MIMO 720F, Corsair Vengeance K90+M95