I don't know for absoluetly shure if this topic might be a repeat of an existing one, only thing I found casually looking through was recomendations for abadonware sites. What I have in mind for this thread is other kind of preservation: not about where to get copies of files of certain games, but more about how to run old games on modern machine. Emulators, tools, fan patches, tweaks, and probably most cool: opensource fan ports of game engines. Currently, on a modern PC, you can run basically almost any games, but sometimes people don't know how. Maybe we can collect here at least some information and offer some help to make the process of playing old games more enjoyable.
Maybe I will start from some usefull basic links:
1. PC gaming wiki is a usefull place to check if there any fan patches, fixes or twaks avalible if you not shure they exist or can't find them casual way.
2. Very awesome list of OpenSource game clones, ie new engines for old games made by fans. Big list of projects - saldy, not full, sometimes not most updated but still, great source to look into.
3. A Wiki about emulators. Also may be not super-detailed in places, but follow updates and development of many emulators, have descriptions, recommendations and lniks to them,
4.The Patches Scrolls is nice resource to search for the patches for old DOS games. If you install them from floppies or from CDs they most often will be not the latest version.
5.VOGONS is forum community about running old games on newer systems. One of the first places in the internet where you can ask direct question about topic about running old games and fix their issues, especially if you not found solutions in other places
Some links on more specific things I using as example:
1.ScummVM. Biggest "compilation" of actual engine ports. Yes, this is not an emulator but set of new engines for old games. Started as re-implementation of SCUMM (a Lucas Arts' 2d adventures engine) it nowdays grow to support like hundreds of games, from text adventures to fully 3d hardware accelerated games. Focusing on Adventures and RPGs, it also may support action and puzzle games if they using same engine as some already re-implemented engine from some adventure game. A lot of games you buy on GoG or Steam have already built-in ScummVM parts to make them run, but it is better to use actual ScummVM to have easy usable list, auto-updates, all menus for configuration. It is because ScummVM why you now can easelly play 256-color FM Towns version of zak mckracken or Blade Runner. Support almost any platorm imaginable.
2.PCem. Awesome emulator of PC hardware. Much better that just virtual machine or something like that. Whad doeas it do? It emulating actual computer hardware - motherboard, CPU, videocard, everything! You building you PC, and congratulations! You have emulation of this actual computer, now you can install any OS you want and use it as full complete PC. Supports hundreds of hardware from original 1981 IBM PC to Pentium II CPUs and VooDoo3 video cards. With every new version there are more supported hardware. Has an active fork, 86box but I never tried it and more than happy with regular PCem.
3.DosBox Game Launcher - good GUI for DosBox. Instead of having multiple dosbox installations, editing dosbox text configuration files you may have this. Have multiple Dosbox versions inside, create profiles for game and all configurations for every game you want in user-friendly way. Well, you may build an actual DOS PC in PCem, but if you are using the DosBox, this is good way to go. Sometimes for specific configurations for games that may requre some specific tweaks it is good to visit DosBox compability pages for game you searching
4.dgVooDoo2 - Good tool, creates custom .dlls that allow games made for older APIs like Glide and old directX work with modern systems and allow some modern API features, like resolutions, antialiasing etc. Absoluetly needed if you want to play some late90s and some early 00s hardware accelerated games and want to play them on modern machine directly, not via PCem or something. However yes, it may cause problems in some games and not absoluetly universal solution, but good enough. Some games have custom solutions similar in the idea and there other alternative glide wrappers.
About GOG versions:
Yes, the GOG offering games that will run on a modern system by default, and usually you can divide them into these categories:
1.Games that run natively without problems - Nuff said, of course, search for fan patches is always a good idea for any game but otherwise nothing to say.
2.Games with some fan patches or installed engine replacement, like ScummVM - still better search for this engine replacement or google the patch. GOG updating it from time to time, but not often, so you may have not the most up-to-date version.
3.DOS Games - usually they have just DosBox attached. And usually not very well if at all configurated. Always check MIDI, render, aspect ratio correction, resolution, etc. option yourself if you don't want to end with a blurry, stretched picture, and fart sound instead of the music. Yea, visiting the compatibility page on the DOSBox site and PC game wiki for optimal settings also a good option.
4.Windows9x games - what I found is that most often there is some sort of outdated glide wrapper, like old nGlide versions. With this old DirectX and 3DFx Glide games use the most up to date dgVooDoo2, or new nGlide versions which you can configure yourself.
Here are some screenshots of things I metioned.