The Hexen wads listed here are the best I have found so far. I have played them all the way through using the Zdoom port with no problems. I have quite a few more that I got stuck on or have had other problems with. If I solve my problems with them and they are good I will add them to this list.
BF Wad has 5 levels. The file is 128KB in size. The file name is hex_bf.zip.
Carnage Galore III: Fury of Vuradi has 30 levels. The file is 7.1MB in size. The file name is fury_ch2.zip. It comes with the Doomsday port. This one gets hard.
Chuxen has 6 levels. The file is 326KB in size. The file name is chuxen.zip.
Dark Realms v3.0 has 16 levels. The file is 4.1MB in size. The file name is DRV3-0.zip. This wad is still in the beta stage. If you get stuck there is a walkthrough available at Filefront. Note: It was made to be run in DOS, or using Dosbox. If you use a port it will have bugs, like HOM.
Dreadnaught and Knockabout has 12 levels. The file is 595KB in size. The file name is k_d11.zip.
Dream of Majic v2.0 (episode 1) was just released in March 2008. It has 5 levels and the file is 30.0MB in size. The file name is DOMep1.zip. It has 2 new players, new weapons, and monsters. It's for the GZdoom or Zdoom ports. I think it's very good.
HexenHub has 3 levels. The file is 253KB in size. The file name is hexnhub.zip.
Hub of Pain has 3 levels. The file is 280KB in size. The file name is colin4.zip.
Shannara has 4 levels. The file is 466KB in size. The file name is shannara.zip.
Starship has 4 levels. The file is 592KB in size. The file name is stapship.zip.
Stonegate has 6 levels. The file is 241KB in size. The file name is stngat11.zip.
Wastelands: Part 1 has 5 levels. The file is 541KB in size. The file name is drkportl.zip.
Wolfen has 5 levels. The file is 5.9MB in size. The file name is wolfen.zip. Note: This wad would not load with the newer versions of Zdoom I have, (v2.1.4,v2.1.7,v2.2.0). But it did work with version 2.0.98.0. I included a link to that version of Zdoom.
World of Zoweseandak has 6 levels. The file is 204KB in size. The file name is zowehex.zip.
I also found an interesting wad called Korax (KMod28.zip it's 3.4MB in size) at the ModDB site. This is not a level wad but a gameplay mod. It allows you to change each of the players (Fighter,Cleric,Mage) stats. Also some items can now be used by only some of the players. You also gain experience as you go along, increasing health,strength, magic, etc. Some of the monsters drop silver bars when you kill them which you can use to buy items at the store between hubs. I think its worth checking out. I placed a link to the ModDB site below. This mod comes with its own port, Doomsday, included. Note: I left the text link to the ModDB site but changed the download link. The download link will now take you to my Filefront page with the Korax file available for download.