I also have Super Quake v1.2 and Jigsaw2 that were formerly created in (I think) 2000 and 1997, respectively. Super Quake has a mace hook, sniper rifle, cluster grenades among other weapon mods, and Jigsaw2 has a collection of weapons, and I think a deathmatch map.
Some historical text messages in Jigsaw2 abound from the late 1990s !
Update: Here are the list of modified weapons in Super Quake v1.2. Select them by hitting the same value key as the original weapon, such as hit the 2 key twice from the shotgun to get the Laser Rifle, then one more time to get the Sniper Rifle:
Axe - Grappler (looks like a mace that hooks/does damage)
The division between single player maps that include some custom content on one hand, and partial/total conversions on the other can be kind of blurry. There are several releases on Quaddicted that could be classified as conversions or mods (https://www.quaddicted.com/reviews/ad_v1_50final.html being a recent example), and include new or modified weapons, monsters, etc.
You can try searching the Quaddicted map database using keywords. This doesn’t always work perfectly (things have not been tagged consistently), but if you do a search for “weapons”, for instance, you’ll see plenty of releases that include new or modified weapons:
http://www.quaketerminus.com/addon.shtml is an old page that lists a few mods with download links (including several releases that are also on Quaddicted; as I said, the map/mod distinction can be blurry). It includes a link to http://www.zerogravity.com.au/portfolio0601.php, by the way (which seems to interest you, based on the other thread you started).
You could also try searching through http://www.moddb.com/ for Quake mods. http://www.quakewiki.net/quake-1/mods/ is another page with a list of mods that can be downloaded (once again including some SP releases that are also on Quaddicted), including Jigsaw2.