Well, it seems that 2012 is a great year for classic wads, unfortunately, that is not my thing. I always look for atmosphere and aesthetics (usually) above all else (yes, I know, gameplay is important, but to me, not as much as the aforementioned wad traits). Not on purpose, that's just what I thoroughly enjoy. Wads like Unloved, UTNT, & Hellground, to name a few, are like the greatest things that have ever graced the Doom world, IMHO (Not to mention Doom 3, which I personally think the authors did a f*!!#*g amazing job with, once again, IMHO). That having been said, I am glad for those who like classic wads, that they finally get a year, wherein, most of the good wads are, in fact, classic.
In short, I nominate the most atmospheric map I have played this year (although, it is not one of my favorites of all time or anything), Beyond Reality.
P.S. Not to be selfish or anything, but I really hope that 2013 has more atmospheric and mood setting wads than 2012. Not to be rude, but I just get sick of staring at the same textures from like 12 years ago. Eternal, Vader, Skillsaw, & Tormentor667 (among others...), keep doing your thing (PLEASE!) :)
I finally had the chance to play Putrefier, and I must say I would like to nominate it, as well.