My opinion changes a lot on the subject frequently but right now I'm in Duke's corner. I used to absolutely love Blood, while still liking Duke but my opinion kinda flipped as my opinion on these sorts of games matured to appreciate the superior things like Duke's enemy lineup, art design and some of its levels. Blood still looks great, the art style and atmosphere is great but the enemy lineup and maybe 35% of the levels fall a bit short compared to Duke. Have to appreciate it for the weapons and powerups (reflective shots kick ass). Shadow Warrior on the other hand I only finished relatively recently when Redux came out - I played through it all, had only played the Shareware of it before I think. Even though Redux came out a few years ago I had played Duke & Blood many years before. Shadow Warrior is still a great game but it had this strange emphasis on Turok 1-style first person platforming (kinda weird, they were released around the same time) in a lot of its levels, for the most part though it's really good and shows off the Build engine at its most advanced, the game incorporates a lot of clever stuff to get the most out of the Build engine compared to its fully 3D contemporaries (prior to Ion Maiden that is).
Beyond the "big 3" it gets a lot harder to read into it. Redneck Rampage is mentioned a lot as the "4th best", but that game has some major fucking issues. I'd say around half of the game and its design is good but the level design ranges from decent at best to downright shit (sewer maze level with near-hidden buttons for required progression, multiple keys needed in single levels that don't even have a different color/door trim color ala Doom, Duke). The enemy design and combat is similar, ranging from decent at best to retardedly difficult (Vixens almost literally hitscan instakilling you makes the later parts of the game pretty savescummy even if you're an experienced player). Redneck Rampage's Route 66 expansion is okay, some of the level design is slightly better than the main game, some of the level design can be seen as worse, it's more of the same. Redneck Rampage Rides Again (the sequel, or a standalone full game's length expansion pack, whatever you wanna call it) is very much improved over the original game, though. The level design there is hugely improved (some of the levels I actually found kinda stunning visually because of how large they were) and it starts to do a lot of interesting stuff with Build similar to Shadow Warrior (vehicles and such). If you wanna bundle all three of these titles into one then you can probably call Redneck Rampage overall "decent, not great".
PowerSlave / Exhumed DOS version is pretty much the unsung hero of this engine for me. That game is seriously good with the DeHacker patch (it improves the controls so god damn much, goes from being nearly unplayable to being my personal "4th best"). Very different game from the console versions (and PowerSlave EX, which is a PC recreation of the PlayStation version of the game) as I understand it, those were all sort of Metroid Prime-style (predates it but you get the idea, sort of Metroidvania-like) action adventure first-person shooters, rather than the classic arcadey Doom/Duke style PC FPS games. The game is honestly impressive considering it runs on a version of Build older than Duke 3D's own, it might not have all of the features that came in later versions of the engine and later games running on it but it still manages to do some cool things. The developers pulled off some really good looking and interesting Egyptian environments, the level design is overall more solid than Redneck Rampage's IMO. The moment to moment gameplay is kinda similar to Heretic, you get items/powerups you can activate to increase your weapon damage, make you invulnerable, etc., it has a mixture of magical and conventional weapons which are all useful and see equal use in my experience because of how ammo is rationed throughout the game. The game differs from just about every other classic 2.5D fps in that it uses checkpoints within levels, lives, autosaves between each level, has no difficulty selection and lets you go back to previous levels from the map screen after you have beaten them. It makes it all a really seamless experience with no savescumming and appropriate balanced punishments for failing jumps or battles with enemies. I'm actually kinda surprised how good the game is once you get the controls to be non-cancerous, everyone always seems to refer to the DOS version as shovelware crap made for the Doom-clone loving crowd, while the console versions are for INTELLIGENT exploration-focused and puzzle-solving gamers.
And further beyond that... shit like Witchaven 1 & 2, William Shatner's TekWar, NAM & WW2 GI, Extreme PaintBrawl, all really terrible/mediocre experiences. The closest ones that get to being worth talking about are the Witchaven ones, but they are laden with artificial difficulty that basically necessitates savescumming... no, not your Dark Souls kiddo "artificial difficulty", I'm talking about shit like perfectly normal looking floors that you can fall through and get one-shot impaled on a spike with no warning or way to avoid it without having fallen into it previously and quickloaded.
Oh... and Ion Maiden is shaping up to be pretty damn good if you ask me. Just basing an opinion on the Preview Campaign, if the rest of the game is anything like it, it's certainly capable of breaking into the "top3" spot ahead of Shadow Warrior for me.
Personally:
Duke > Blood > Shadow Warrior > PowerSlave / Exhumed > Redneck Rampage series > *
Sorry for blogging.