Yeah, PCI Express is more or less "another generation" of PCI; it's faster and has additional capabilities. In particular, in this context, it's fast enough to replace the AGP connection on which graphics cards used to rely because the main bus (e.g., PCI) couldn't handle the necessary bandwidth.

And also yes, "Hyperthreading" can indeed slow down a lot of parallel jobs, because the so-called "threads" are fairly simple. Most CPU chips for a long time have been pipelined and parallelized -- they can issue multiple instructions while waiting for others to finish. Hyperthreading lets the chip designers say they can fill more of those instruction slots simply by adding an extra instruction pointer (PC) and some control logic. However, because a lot of the chip logic (including most cache memory) is shared between the "threads", they do interfere with each other.

Poser isn't multithreaded (even Poser 6, so far as we've heard), but much of the OS stuff, including graphics and file access that happens as a result of Poser will run in separate OS processes or threads, and therefore, if you're lucky, Hyperthreading may speed things up a little.

Since Poser 6 can use OpenGL for previews, a fast graphics card on PCI Express might be able to render a little faster than an AGP card. But you're unlikely to notice much difference unless the scene has an enormous amount of geometry and textures... or possibly if it can render realtime animation previews with full texturing.