86box has more features, and the latest version comes with a frontend. PCem updates are long in coming, making its forks preferable (just like DOSBox).

I've used DosBox, VMware, VirtualBox, MSDOS(vm), 86box and PCem to run DOS stuff on non-DOS systems. I still do most with
DosBox, but for faking a "real" system, I've settled more on PCem. I found 86box tougher to setup and tweak, but it really
depends on what you are doing. If you need to get optimal performance/compatibility (like much gaming), you prob would do
better with the more capable/complex ones - I'm mostly just testing stuff I've written an typical old systemss, and
find PCem best (for me). I don't really care about slow release times - The systems I'm testing on haven't been "released"
in decades - so far not encountered any critical bugs which need immediate fixing.

So I scoped out 86Box recently, and was enormously impressed. It now lets you mount folders from the host system in the virtual CD-ROM drive which is a convenience I'd been longing for. I was curious if the mouse felt any better, and I didn't think so? But it seemed no worse than before, and about the same as PCem. I don't know, maybe my system isn't fast enough to benefit from that. I only have a 5800X3D. The shaders for 86Box are nice too. If you use the OpenGL renderer you can specify the GLSL shaders you want to use directly from the application. If you use the Vulcan renderer you can use something like Reshade to get really fancy.

Performance for me seemed the same as it ever was. PCem and just about any version of 86Box seems to max out around a P233 MMX for my host system. There might be some changes in performance on the margins, but I wouldn't expect a new class of performance out of any version of these.

I use 86Box on Linux because it has a flatpak available.

For networking PCEM only has 10 Mbit support while 86Box has 10/100 Mbit support.

Huh? No Gigabit ethernet yet? How comes?
Doesn't, for example, Intel Gigabit-Ethernet-Controller 82574L have DOS support?

I mean, 10 or 100 MBit/s isn't exactly much.
If you divide by 8 (Bit to Byte), it's about 1,2 Mbyte per second, or 12 MByte per second, respectively. On paper, without overhead.

In practice the bandwidth is about a bit it more than half of that.
So 700 KB/s (a DD diskette) or 7 MB/s. Not exactly quick.

Way back in the 2000s I found it funny that DSL was slower than transfer rate of a floppy controller.
Or that then-fast 10MBit cable internet connection was the maximum speed of an 10Base2 NE2000 card from 1987.
Even ISA bus from 1984 was faster than that (16 MBit/s theoretical).

Edit: I did’t meant to criticise the authors of PCem/86Box here.
I've just assumed that various network adapters had been emulated a dozen times in the past 25 years or so (in different projects)..

As far as I know, there haven't been any changes to 86Box's underlying emulation performance, so PCem should still provide somewhat better performance.

Honestly, in 2025 I’d lean toward 86Box for gaming. PCem was solid back in the day, but it hasn’t had a proper update in years. 86Box v5 looks like it actually fixes a lot of rough edges, smoother mouse, better display output, more hardware options, which matters a lot if you’re running games on Win95/98/XP.

PCem might still work if you already have everything set up and tuned perfectly, but for new setups or better compatibility, 86Box seems like the safer bet now. I’d try it out with one of your old configs and see how it feels, chances are it’ll handle your games just as well or better.

I personally use dosbox-staging for gaming (due to the dynamic shaders) and 86Box for MS-DOS development (serial support FTW).

But if you don't want to use dosbox, then PCem and 86Box are mostly equivalent, with PCem being a little faster if you are emulating powerful systems (from P90 onward), probably at the expense of some accuracy. The biggest difference you are going to find is the UI, honestly.

I have only tried PCem and while it was great, i noticed it corrupted my images, which was a real pain because I had to reinstall EVERYTHING all over again, then I gave it, but this was a few versions ago.. or maybe I was doing something wrong. Either way was fun, I even setup an OS2 Warp setup to try it out

86Box has come a long way and is continuously updated. I can even run a Pentium II 233MHz with Voodoo 3 at 99 - 100% all the time without stutters in my Ryzen 7 8845HS laptop.

Of course, for hardcore demanding 3D Win9x era games, I'm using QEMU with SoftGPU.

But for the rest, the Voodoo emulation is good enough, and I mostly play the RTS games in the Pentium II "system" - like Fate of the Dragon.

It's my go to emulator for all my PC needs. I spend more time with 86Box than tinkering with real classic PC because of the convenience of trying out different "systems" even during work breaks using my laptop.

And 86Box now supports way more, more systems and hardware than PCem.

I'm using Debian and using the nightly latest AppImage build of 86Box from Jensen website.