Well, though I'm an old Doomer, and started my way on Doom forums - I wasn't following the Doom scene in recent years, so donnow to which extent I can he helpful.
Sure our of my memory I have fond memories of "Knee Deep in ZDoom", "Action Doom", "Brutal Doom", "The Darkest Hour", "ZBlud", "Batman", "Simpsons", "GhostBusters", "Equinox"....but I'm at work, I might look at my old zDoom directories to remember more names.
"StarWars Doom" is probably too old to mention...
Out of those, I also think KDiZD, Darkest Hour, Batman, and Equinox are done very well. Seems like you are a biggest fan of total/partial conversions over plain add-ons, which is no problem.
I must comment that I seriously think a LOT of people on Doomworld seriously underrate KDiZD because they complain about switch hunting or how hyped it was, but regardless I played KDiZD one time and had a lot of fun in doing so even if there was an occasional point I was frustrating (once or twice not knowing what to do next) and it doesn't really have the original E1 vibe, but I just interpret that to be a modern remake, not necessarily aiming for identical feel. BTW KDiZD had a bonus levels you might not have played - open the console and type "map z1m0" to find out.
In keeping with the idea of total/partial conversions, I must also recommend the following from the past (approximately) five years to you:
-The Ultimate Torment 'n Torture (wow, today is EXACTLY its fifth anniversary!)
-Action Doom 2 (liked it much over the first, VERY different, COMPLETE total conversion) (2008)
-Cold as Hell (2008)
-BGPA Missions: Liberation (2008)
-Arcadia (A BioShock level converted to Doom!) (2010)
All of these recommendations were wads I have played, but they have been recited into my minds thanks to yearly awards given to the best wads. There are 10+ each year and to find them, go to the URL http://www.doomworld.com/xxyears where xx is an integer between 10 and 18 (with the range expanding up by one on each passing December 10). While I don't think every wad listed on these pages is fantastic, and also I think they miss some really excellent ones residing in the archive, overall this is a VERY good starting point if you want to expand your library of good Doom wads.
EDIT: Warning, clicking on the URL link will take you to a nonexistent page, you have to replace xx with an integer as described above.