From my experiences, the BSG mod is definitely one of the most demanding Nexus mods out there. I think it has to do with all the particle effects, which the engine just doesn't handle all that efficiently... but that's only a guess of mine. At times it stutters for me, too... also happens for me in some other mods, including my own Freespace one, although more rarely. I don't believe it's much of a hardware issue - more an issue of the modders overdoing their effects beyond what the engine is capable to handle.
The only actual issue I ever had was years ago with older Nvidia cards (or maybe it was related to the drivers back then): when enabling the "fullscreen glow", performance would go downhill really bad... from a perfectly smooth 60+ or even 100+ to 30- fps, for example. Similarly powerful Ati cards seemed to fare way better, so I suspect some driver or hardware compatibility issue.
I currently have an Nvidia card (GTX 460) and don't experience this issue anymore.
Also I don't believe Nexus is very optimized for multicore processors. On my quad core, I usually see one core being heavily used (90-100%) and the other three only mildly stressed (ca. 20% usage). The game was released in 2004 and the first dualcore CPUs appeared on the market in 2005... and it even took a whole lot longer until their mainstream breakthrough.
