But system friendly RTGd app like something like 3D rendering app in OS 3.9 but not requiring UAE to execute it is faster on Amithlon no?
No, it's very close to the same, in fact most of the code is shared. Also, WinUAE especially is pretty finely tuned, has many more years of development and can take advantage of drivers that have been optimized by the company that made the hardware. The Amithlon graphics drivers are reverse engineered and just a little more than a framebuffer, not much hardware acceleration.
I am buying the hardware from ebay anyway.
Soundblaster 128 PCI, Realtek 8139 PCI yes?
Graphics card...which is best?
One more question, right now I am transcoding 21 VIC20 videos AVI==>FLV and set task priority to lowest and watching Terra Nova on movie player with priority set to high and XP isn't doing a good job as video playback is jerky!!!! Does OS 3.9 suffer like this or does it have true responsive preemptive multitasking ?? 
Most of the CPU time will be spent emulating a 68k CPU, so don't expect miracles.
Think of it as a cheap hyper fast Amiga, like a PPC system. It's never going to be as fast as a native x86 machine, OS and software because it has to spend time pretending to be something else.
Don't get me wrong, I love Amithlon, but you have to like it for what it really is.