What John Romero released are .map files, which basically are "source codes" of all the Quake maps. However, what he did not release are the textures, which are also contained in the resulting compiled .bsp map files. This is the core problem of the whole thing. Let's see what are it's consequences.

1. Alright, let's take the sources, compile them and we have free .bsp
As we've just said, we don't have the textures. Without textures there's nothing to display on the walls basically.

2. That's easy - take textures from the original maps, everybody does that when creating a custom map anyway
That is right. Creating a custom map with textures made by id Software is allowed by the Quake license. So we are free to use the textures and we have the source code under free license. Sounds good, right?
Here's the biggest paradox of this all. Because the source code is now under GPL and textures under different license, these two things can never be compiled together.
Spike: "GPL prohibits license mixing with such licenses."

3. That's truly sad. But we still have Quake Retexturing Project, so at least we can use their textures?
Those textures are made by persons outside of id Software, are not under any strict license and are quite faithful to Quake look and feel. And that seems to be a problem here. Those images are not perfect digital copies of the original textures, however are clearly created by taking the original ones as a base and improving the details. It resembles Quake feel and look and is derived from the original textures.

4. Oh right, so we are doomed, backup plan failed? We simply can't use anything we have?
That luckily is not right. Todd Hollenshead from id Software who gives interpretation of license agreements explicitly allowed free stuff:


So yeah, the real last backup plan exists. Free maps can be produced. Most probably they can't resemble Quake feel and look in details though. But anything else can be used. Solid-colored walls for example. Such bsp files are already done. Or some completely different theme can be used too.

How would it work? You have to have exactly the same .bsp file as the server has to be able to connect.
That has already been taken care of. The server can be changed so that it recognizes when the client is using an alternative free bsp model and client can connect in such situation. The code is already done and is present in the ZQuake project at the moment, all done by Tonik.

All the conclusions in this article are based only on opinions of various people on forums, especially Baker5, Spike, LordHavoc and Tonik. Since there is very low amount of lawyers among Quake players, one can never be sure which interpretation of the license is true.

One of the many opinions for example is that derivate works such as Quake Retexturing Project are not an issue here and can be used in the "final free maps" pack. And there are efforts in QRP to finish all the missing textures so that new bsp files can be compiled using QRP textures only. It is an open matter to get clearance on this and to unify the efforts of creating the final free alternative maps.

How to get out of this? Maybe ask John Romero to release the .map files under some different license? Are id Software's intentions really to make our lifes that much complicated? What was the point in releasing the .map files under this license? Doesn't the community maybe deserve something more? It certainly is the community who keeps the game alive for more than a decade already and mostly thanks to this id Software still can sell this game for money.
On the other side not many companies do as much for open source as id Software and we can also quote John Carmack from the Gamers With Jobs Interview:

If the community decides for the fourth, last plan mentioned here, the main point of this effort would most probably not be achieved. That is attracting new players. Single-colored maps would most probably not attract new players to the game. Maybe there is a place for a project "in between" - not problematic QRP textures and also not solid-colored ones, but a completely new textures with a new look, maybe a chance to give Quake a brand new e-Sports feeling...

But then there are also other problems. Original bsp files contain additional information that are not in the .map file - texture size, placement and offsets, that's another complication for QRP case. Also most people presume that shareware Quake is free. Shareware version has a special kind of license and then there is a problem of distributing things under GPL together with things under such license. This pretty much affects the nQuake project.

More reading:
John Romero: sources released
Inside3D forum talk
QuakeOne forum talk
quakeworld.nu forum talk + GPL maps from Baker5
Quake license