VirtualBox and Virtual PC
Perhaps I am the last person in the world, who will prefer VPC over VBox, but when we are talking about Windows 3.x, VPC completely win. This is because VPC is emulating S3 Trio 64, which is very well supported (with 3rd party drivers) in Windows 3.x environment, network card and sound card are working very well too. I have installed Windows 3.0, Windows 3.1 and Windows 3.11 in QEMU, VirtualBox, VMWare Workstation, Parallels Workstation, Bochs and VPC 2004, 2007 (just because I can, as someone said before) - both with TCP/IP support and installed internet browsers. Not very usable, but works...
VirtualBox doesn't have Windows 3.x guest additions (and Windows 9x too, sadly...), its emulated graphics hardware lacks of any drivers for Windows 3.x, I tried to use VESA patched VGA driver (it still can be found in some internet sites) - with various success, because it works but very slow. In fact, I found drivers for Windows 9x (VBEMP - for some old video adapters and for emulated VirtualBox adapter), but they were very basic (unaccelerated at all) and damn slow in Windows 95/98/Me.
So, VPC 2004 and especially 2007 won the battle for Windows 3.x emulation.
VPC also won in my OS/2 tests - I succeed to install and use OS/2 in VPC 2007 with and without hardware virtualization. I was unable to install successfully OS/2 in all other virtualization software, except in Parallels Workstation, but only with hardware assisted virtualization. And it was not so stable in Parallels. This is strange, because Parallels was founded as OS/2 virtualization software.