Which encoder you use depends on what you want out the end.
JROK - Sony CXA-based chip and works great with many boards. It is, however, incompatible with a small percentage (can't remember which)
R2N/NeoBitz - both are AD724/5 based and work similarly for S-Video and composite with the obvious difference being the component video circuit. Most find that the Analog Devices IC works best for Neo Geo, but is incompatible with more boards that the CXA chipsets.
I myself use all three of those encoders, depending on project. High end superguns I always go with the NeoBitz since the component video has very very high compatibility and the S-Video/composite is treated as a bonus. R2N for Neo projects that component isn't needed. JROK for standard superguns.
I build my own encoder from scratch as well, based on the Sony CXA chip. I use it nearly exclusively for Turbo Grafx/Duo/PC Engine applications and it's awesome. Why don't I use the JROK then? Myself and others have found that the JROK has some issue with these systems, which I'm trying to solve. The hardest part of building your own encoder is getting a good chip for it and then wiring it. The 1645 requires more connections that the 2075 version, but works well when properly installed. I have my process down to 50 minutes per encoder.