I wasn't much of a PC gamer until Windows XP so I can't comment on how one performs over the other for Windows 9x. I did lots of DOS gaming in the 386/486 era and when comparing ease of setup DOSBOX is superior. I have a lot of (mostly unpleasant) memories of how much 'fun' it was tweaking DOS to work with games that required too much base RAM, didn't like EMS, didn't like my video card, etc. PCEM/86BOX, VirtualBOX, VMWare all duplicate this experience.
DOSBOX is breeze - No virtual HD images or DOS required. Copying/updating your DOS game is a breeze since you are mounting a subdirectory in your host OS. Some games will work out of the box with the default configuration. Other will require fine tuning the CONFIG file (DOSBOX allows you to have individual config files for each game). I have been able to play all my old favorite 386/486 DOS games in DOSBOX on my Windows 10 PC. I haven't tried DOOM/DUKE3D/WOLF3D/DESCENT2 because
A) I read that performance-wise the experience isn't good
B) I have modern Windows ports of those games
I may at some point try and setup Win9x in PCEM just to see if I could get it to work. One thing I don't like is having to rely on a third party tool such as WinImage just to be able to import/export files to/from the HD image.
I did manage to setup PCEM with DOS 6.22 and Windows for Workgroups 3.11 and networking. I wanted to duplicate the setup I had in MS Virtual PC (Ok, I cheated, I imported the MS VPC .VHD image into PCEM and just changed a bunch of drivers). Still, I did get it to work.
WFW 3.11/Netscape Navigator Gold 3.0
Arachne for DOS Web Browser with DOS PKT driver