There's quite a few capitalised functions, including some pretty commonly used in functional programming, some statistical tests, and all the Sys. functions. Here's a (not exhaustive) list of some that might get used semi-regularly:
AIC, BIC, C, Find, Filter, HoltWinters, I, a bunch starting with Kalman, Map, Negate, Position, Reduce, Sys.Date, Sys.time, Sys.info etc, Vectorize, X11.