The game ALfheim Online (ALO), which was the focus of the second half of S1, was developed based on the server and code from Sword Art Online (SAO).
After Argus went bankrupt due to the Sword Art Online incident, its servers and data were acquired by RECT Progress Inc. and used to create the VRMMORPG ALfheim Online.
As ALO is based on the core programming of SAO as a complete virtual reality MMORPG, the ALO system is capable of rendering the entire ALfheim environment with incredible realism, extremely similarly to the level of SAO.
At the end of S1, the so-called Seed was released, which was basically the developer toolkit for SAO, allowing everyone to create their own FullDive games (for example, Gun Gale Online, which was the focus of the first half of S2, or Underworld).
The Seed is a free, preset series of program packages that can be used for creating Virtual Reality (VR) worlds as well as control the input and output of the five senses of the players, allowing players to FullDive into the created world.
«The Seed» includes the basic programs needed to create a VR world, such as the audio and video system, as well as a downsized version of the Cardinal System, which was used in Sword Art Online to help in the development and to maintain control of the game.
Is anyone still playing (safe versions of) SAO?
Yes. At the end of S1 they added a copy of Aincrad (the world of SAO) to ALO allowing the players to play through it (creatively named New Aincrad). For example, the Mother's Rosario arc takes place in New Aincrad. On a side note, the original SAO itself was theoretically safe to play. The dangerous part was the hardware in form of the NerveGear. Playing it with the newer AmuSphere should be fine, except that you can't log out (but if someone else removes the device, it should work).
What references are there to SAO s.t. SAO is still 'indirectly' involved in the actual series?
Since, as far as I know, every FullDive game is at least indirectly based on SAO's code, you could say that the original game is still indirectly very relevant to the series.