Hi Dave, I'm very envious of that A1200 system you're building up! If you plan on trying OWB or Netsurf on it, you will need a graphics card too, neither of them work with AGA.
As for running those browsers through emulation, I've not tried it yet to be honest. I don't use Windows at all, so no WinUAE here. I do run Aros natively on two PCs though, and OWB is great for using on every website I go to. It can't play inline flash videos, but it's not hard to open them with MPlayer instead.
I'd say Netsurf would be the better choice for running through an Amiga emulator though, and OWB for Aros.