Late reply, but like 8007 said, DOSbox focused on getting things running with lots of hacks and game specific settings. This wouldn't be an issue if they were still updating, but the last time DOSbox updated was years ago. It's "good enough" if it works, but that's about it. PCem is still under active development and is getting more accurate and faster as time goes on.
Meanwhile PCem has been focusing on trying to emulate every part of the hardware as 1:1 as possible. So instead of having a generic motherboard, generic graphics card, generic SB card and so on, PCem uses specific emulated hardware. So instead of generic mobo with generic CPU with a set clockspeed in settings, you would use say…. an ASUS P/I-P55T2P4 mobo with a Pentium MMX 166 CPU. You can go into the BIOS for this emulated mobo, and change any setting just like on real hardware. You aren't using some generic VGA card, you are using a Phoenix S3 Trio64 2D accelerator that can handle 16M colors at 1024 x 768 in Win3.1, paired with emulated VooDoo cards in SLI. Naturally, having actual real hardware emulated means games tend to run the first time without any special settings needed. DOSbox uses an emulated hackjob version of DOS. PCem will use any OS that you install on it. You wanted DOS 2.0? Go ahead and use it. You want to use DOS 6.2 with DOSSHELL backported to it and set to automatically run when you turn it on? You can set that up easily.
With DOSbox, you have to individually configure each game, but you don't usually have to setup the environment. With PCem you MUST setup the environment(install drivers for everything, install the OS, etc), but the majority of games the OS can run only requires you to install the game. While DOSbox is faster to setup to get a single game to run, PCem is faster in the long term for DOS/Win3.1 emulation. Once you have your DOS or Win3.1 box setup, all you need to do is mount the install disks and install the game and play.
The only downside to PCem is that it requires you to know what you are doing, where DOSbox is brain-dead easy, doubly so if you are using a front-end like D-Fend Reloaded. If you don't know how to manage memory in DOS, you will have problems getting the memory hungry games to work. If you don't know how to deal with memory beyond the 640k, you'll have problems getting Win3.1 games to play. It helps to be familiar with where to find drivers for old hardware, and various old software designed for DOS/Win3.1. The plus side is PCem can play a lot of stuff DOSbox can't. Ultimate Domain/Genesia's CD-ROM version ONLY runs flawlessly under PCem. DOSbox chokes and crashes, and stuff like VMware locks up shortly after the game starts.