You are correct, Matt, that using /3GB reduces NON-PAGED pool space by half (from 256 MB to 128 MB). It also reduces PAGED pool from about 350 MB to 250 MB.
Large tokens have the most impact on PAGED pool memory rather than on NON-PAGED memory. It is true that tokens require some NON-PAGED memory, but the impact is much less than on PAGED memory.
As far as PCI-Express goes, it "steals" some address space beneath the 4 GB boundary. Typically this is 256 to 512 MB. For a machine with 4GB of physical RAM, this makes that amount of RAM unuseable/unaddressable.
You can use /PAE to "unhide" the RAM. Yes, this will use an increment of kernel resources. Unless you're on the ragged edge already, it shouldn't be that significant. But unhiding this RAM is unlikely to provide any significant benefit either to the server's performance.
You can test exactly what happens on your particular machine by booting with and without various memory tuning startup options. For more detail about PAE and Exchange, see this previous blog entry:
http://blogs.technet.com/exchange/archive/2005/12/14/416065.aspx