XFree86 releases starting with the 3.2A beta are based on the X Consortium's X11R6.3 (the final release from the X Consortium).
R6.3 is an update to R6.1, and is intended to be compatible with R6.1 and R6 at the source and protocol levels. Binaries should be upward-compatible. X11R6.3 includes some new Xserver extensions: SECURITY, XC-APPGROUP, XpExtension (print extension), and an updated, and standardised version of LBX. X11R6.3 also has new standards, including RX (X Remote Execution MIME type), and a proxy management protocol. X11R6.3 includes support for gzipped fonts.
R6.1 is an update to R6, and is intended to be compatible with R6 at the source and protocol levels. Binaries should be upward-compatible. X11R6.1 includes some new Xserver extensions: DOUBLE-BUFFER, XKEYBOARD and RECORD.
What about R6.2? X11R6.2 is the name given to a subset of X11R6.3, which has only the print extension and the Xlib implementation of vertical writing and user-defined character support in addition to those features included in R6.1.