Both HoMM and HoMM2 has it. At least my installs do, it may very well be removed in a later updated installer.

I don't have the GOG versions of these, but wasn't HOMM 2 a Windows game, or at least it had a Windows executable along with the DOS one, could they have experimented with GOGWrapper for the Windows executable but concluded that the DOSBox version was more stable, but left the Windows files in for those who want to try them out?

One reason not everyone experience these crashes could be that it seems (to me at least) that dual core systems causes these problems more often than CPU's with 3 or more cores. I haven't tested this idea much, but I've heard that the game Frontlines: Fuel of War (not available on GOG) was nearly unplayable on dual cores, but worked fine on single, triple and quad core machines (only tried FFOW on a triple core machine, and haven't experienced any problems with it, the support forums for it is full of people with issues with it on dual cores though).

Doesn't mean others wouldn't. I thought it was half the reason we all buy here...plenty of games don't work on newer OS' natively.

The shortcut installed to the start menu point to gogwrap and launches the game in DOSbox. The only Windows EXE's installed are gogwrap.exe, Graphic mode setup.exe, unins000.exe, and of course dosbox.exe. The three relating to the game are all DOS; editor2.exe, heroes2.exe, and install.exe.

Well, the best reason is that I don't get screwed with regional stuff. For me at least. :p

I had a problem with the core affinity in Painkiller. Basically the game would run too fast, then occasionally it'd slow down then speed back up. It was kind of jittery.

Well, I have no idea about the purpose of that then, I looked through some of my GOG shortcuts and while most of the Dosbox games don't use it, a couple of them had the GOGWrapper, like M.A.X. 1 and Rise of the Triad. Looking at the shortcuts for the non-GOGWrapped DosBox games, they do have quite long launch arguments,Duke Nukem 3D for example has this: "\GOG.com\Duke Nukem 3D\DOSBOX\dosbox.exe" -conf dosboxDuke3D.conf -noconsole -c "exit". I suppose they occassionally use it to simplify that, and just don't use it consistently.
I did only guess about it's purpose for the other games previously, but to me it would make sense for it to also work as a wrapper for deprecated DirectX versions, since some old Windows games make use of function calls for these, and the only way to get the original releases working on a modern computer is most often to install a third party DirectX or 3DFX Glide wrapper.

I did a little snooping around with the one that comes with HoMM3, and it looks like an AutoHotKey script.

I'm not (yet?) sure exactly what it does (other than launching the game), but you won't find any useful command-line options.

Especially for the dosbox games, I never start these games as deployed by GOG.com because I run a Linux system. Instead of purely running the enclosed windows dosbox, I have a native Linux dosbox that I use to start these games. E.g. the pinball simulator "Timeshock" is crawling with the deployed starter as Wine (the WIndows API layer for Linux) has to emulate dosbox and the game running with dosbox). When I start timeshock with the native Linux dosbox, it runs as expected: fast and smooth. :-) For this reason, the start options and command line parameters are important for GOG.com users with other operating systems than Windows. And as most of the GOG.com games work on my Linux machine (either out of the box or with a little adjustment), I am a happy customer of GOG.com. It's amazing how even games with high demands for 3D graphics and effects run very smoothly on Linux.

Since the only command-line option ever used for gogwrapper is GOGGAMENAME (of course, substitute GAMENAME accordingly, always starts with GOG however), and the GOG installer adds registry keys with the same name containing various settings (among other things, command line options and game launcher exe), I'm pretty sure gogwrapper simply looks up the settings for the game in that key.

I forget where exactly the kays are stored and can't look it up at the moment as I'm at work, but search the registry (in Wine that'd simply be plain-text .reg files, if I remember correctly) for GOGPACK and you'll find the location (those starting with GOGPACK contains information for a complete package, those starting with just GOG are for each game).

HKLM -> Software -> GOGcom = 32bit Windows
HKLM -> Software -> WOW6432Node -> GOGcom = 64bit Windows

If we are talking about the same stuff.

That's the one, yes