Should I run 1/2" pex from a manifold to each fixture or 3/4"?
The average fixture has no need for 3/4" inch, particularly with homerun piping from a manifold. 3/4" is really only needed for tub fillers with larger tubs, or showers with multiple shower heads.

Running 3/4" hot water lines to fixtures will significantly increase hot water wait times, and should be avoided when not necessary (and for lavatory sinks, I'd strongly recommend 3/8" hot water supply lines).