MagJack for PoE Powered Device
What would be best Design (1 or 2) for my application?


Design 2 gives your system more tolerance for miswiring, which is a good thing.  These days it's generally not necessary to pay attention to whether wiring is straight-through or crossed over, because with widely available gigabit and auto-MDI/X the hardware just figures it out.  Design 2 will be similarly tolerant, and will work even if pairs are crossed over or otherwise mixed up.  


  The MagJack that I have been considering, Is it suitable for PoE (Mode A and Mode B both)?


It appears to be designed to support PoE, given the way the center taps and extra pairs are brought out and labeled in the schematic.


  The last question could be a stupid question but still I want to be sure before proceeding further. I was using this MagJack in earlier version of my PCB and it was working perfectly. However, I am moving with SI-52003-f Magjack for PoE capabilities. Will it make any difference for the Ethernet Controller if I switch the MagJack?


No, it won't make any difference.  Ethernet magnetics are all pretty much designed to do the same thing, and the PHY will be designed to tolerate a wide range of cabling characteristics anyway, so the magnetics will make little difference by comparison.