Nehahra because it's less beardy-weirdy. 

I don't think one can compare them. But if you forced me to name my favourite it will be Nehahra* because it is closer to my interpretation of what "Quake" is.
I am just not that into the fantasy setting of SOE.

*Not without "nomonsters 1" though... 

SOE 

Very, very hard to say, IMO you can only properly compare them if you look at both Nehahra's and NSOE's source and get some idea of the ongoing work behind the latter. The vision behind Nehahra is immense (the commitment, too), but the vision behind Drake/NSOE is also rather big. And Drake is just emerging, it seems that NSOE is only the tip of the iceberg. The source had my eyes glazing over - the RMQ defs.qc is bloated, but not as bloated (in a good way) as Drake's. PM is probably just as godlike as Mindcrime.

I'm not going to vote, as it's not the end of the day yet. I don't want to put one above the other, either.

I would like to say that Quoth is also very good in most ways, and I would like to give my huge respect to Kell & Co. as well. It can't really be compared to the other two, though (perhaps it can somewhat be compared to Drake, but not to NSOE). 

though I think the coloured lights and the stained glass windows looked freaky :P 

Pre-pubescent topic. 

Hehehe. You said pube... 

Did the completely worked out storyline of nehahra vs. the simple story of SOE factor into your decisions at all?

As for me, Although I have played SOE and I still not finished with nehahra, so cannot judge at this point. 

I consider it an honor to be compared to Nehahra. The Seal of Nehahra was one of the best things ever done for Quake, it was staggeringly, mindfuckingly good. I felt the game itself wasn't as good as the movie, although the cinematic quality and modding was far better than the original SoE. Nehahra felt like an attempt at making a sort of Ultimate Quake, with many improvements (some of which I didn't like), and a coherent story (which Quake lacked, and it was FASCINATING to see Mindcrime tie all these spooky weird Quake elements together coherently). SoE on the other hand was indeed "Weirdy-beardy" (lol), a shot at taking a single element of Quake design (medieval) and running with it, just as numerous mods have done for Base, or Quoth did for Lovecraftian. I prefer my own maps, although I recognize their limitations and flaws; Nehahra to me had too many different map styles and never really achieved a sense of place. The original SoE in my view did the coherent style, episode-unfolding, sense of place well, but on the modding side Nehahra makes it look like a glorified mappack (which it was). It depends on personal taste, both in mod type and environment theme. With NSOE (and my current projects), PM is really changing everything and a lot more is now possible on the modding side.

Some time I'm gonna get drunk and watch Seal of Nehahra again. Also, is Obscurus dead?