In theory, you could run Quake on any of these machines, even the DOS one - the original Quake release was a DOS program, after all. However, modern engines fix bugs and issues that the DOS and original GLQuake versions have, on top of having other functionalities.
First things first, grab a copy of Quake, either the original Quake CD if you can find it or a downloadable version. I’d recommend the GoG download because it is DRM-free, unlike the Steam download. Maybe you can try the online version on your Win98 system (it has a Glide executable), but even then you’d be running a very old version of GLQuake that hasn’t been properly fixed or even maintained since its release back in '97.
If you grab an online copy, you need to download the music separately: it wasn’t included for legal reasons. You’d be really missing out if you played the game without it, as it’s such an integral part of the Quake experience and enhances the game’s atmosphere greatly. You can get it here: http://quakeone.com/forums/quake-mod-releases/finished-works/7337-high-quality-music-packs.html
Note that it comes in a .pk3 format that is just a renamed .zip archive. Some engines have built-in .pk3 support, some don’t and will require you to unpack the files.
To run Quake in a modern engine, first install the game normally. Go in your Quake folder (usually C:\Quake) and navigate to the \id1 subfolder. There, you should see (among other files and folders) two files named pak0.pak and pak1.pak. These are the game data and the only files you’ll ever need from this install, so store them somewhere (on the desktop or wherever you want) and now you can uninstall the original game, you won’t be using it. Storing these two files in a safe place will save you from repeating this step if you need to reinstall the game.
The next step is to download an engine and this is where things can get a little hairy for newcomers: After id Software released their source code under GPL licence, A LOT of new Quake engines, collectively called source ports, were released by the community. Many are now outdated and unsupported. Of the still actively developed engines, two major branches can be differentiated: the FitzQuake family (QuakeSpasm, Mark V…) tends towards more faithfulness to the original pixelly look while engines like Darkplaces and FTE are more geared towards the bling and a more modern look, with support for real-time lighting and HD replacement content.
The most commonly used today are QuakeSpasm (QS) and Darkplaces (DP). If you choose to go for a faithful look, I recommend either QS or Mark V. Mark V came out of beta stage only very recently, so it might still be a little buggy. It also only supports .mp3 audio files for now, so the .ogg music that you’ve downloaded will need to be converted. QS works very well and supports .wav, .ogg and .mp3. All engines should support the original CD music if you insert a Quake CD in your CD player.
If you prefer the bling, DP is a great engine but its configuration can be a little daunting and its creator LordHavoc doesn’t offer support to its users who are pretty much left on their own. However, many Quakers use it and you can find pretty much all the answers to your questions on the forums, notably at QuakeOne.com. FTE, on the other hand, is much more confidential but its creator Spike is more than happy to help you with any issue you may encounter (note that Spike is also the author of a recent QS fork called QuakeSpasm-Spiked or QSS).
Once you have an engine, install it (usually the instructions are in the readme), create an \id1 subfolder inside the engine’s installation folder if it’s not already there and copy/paste the two .pak files into it. That’s it, now you can play. For the music, there’s no real standard and the procedure depends on the engine but again, the instructions should be provided.
I recommend that you try several engines before settling on your engine of choice. If you’re REALLY bent on installing Quake on your Win98/Voodoo2 system, I asked around and the answer I got was that MAYBE FitzQuake would be able to run on it. However, no-one seemed to really be sure, not even the engine’s author. Also, Fitz is no longer under active development (last build 0.85 is from 2009). For this reason among others, you’d probably be better off installing Quake on your Win7 machine - especially if you’re interested in HD content, as it can drastically drain your system’s performance down.
Mark V: http://quakeone.com/markv/
DP: https://icculus.org/twilight/darkplaces/files/?C=M;O=D (the latest autobuild should be at the very top of the list)