After updating to 1.0.1 some packages seem to be missing. OpenNTPD and siproxd are two that I am looking for that are no longer listed. Are they no longer being supported or do I have something misconfigured?
have a look at the latest snapshot and you'll find openNTPD included in pfSense…
Depending on the version you run you see more or less packages (some packages need yu to be at a special version). openntpd should be there. However siproxd is broken afaik and is hidden atm.