I have MSI 925XE Platinum motherboard & Intel Pentium 4(550) 3.4 GHz Processor. I want your suggestion about upgrading both motherboard 7 processor
For motherboard MSI 955X Platinum or MSI P4N Diamond or Intel® Desktop Board D955XBK. For processor Intel Pentium(630,640,650,660,670) EM 64T. Kindly help me out for choosing these also tell me that Intel® Pentium D series processor is better than Intel ® Pentium ?

The Intel Pentium D series processors are the newer socket 775 units. They should, in theory, be better because they're a newer design but I don't know what specific technology improvements there are. The "Intel Pentium" processors that you refer to could actually mean almost any Intel processor made since about 1994 but I would assume that you're talking about the older Pentium 4 processors that use the socket 478 format. I would expect that you couldn't get that format in 64-bit processors anyway though so, if you're still confused, you might have to tell us where you're looking at these two apparently different ranges so that we can see for ourselves.

With regards to the motherboard, it doesn't sound like the cost is a particularly significant concern to you so, in that case, I'd definitely recommend Intel motherboards as a general statement. You do pay for the extra quality but, boy, you do get a lot of quality!