The last version that had any significant "cool stuff" that 31.25 doesn't was 40d, and the "cool stuff" that 31.x versions have that 40d doesn't vastly outweigh the reverse. The only significant stuff 40d has that 31.25 doesn't were bottomless pits, chasms, underground rivers, dungeon masters, and wagons. Bottomless pits and chasms were basically just tiny caverns with infinite garbage dumps in them. Underground rivers were mostly just underground water sources and triggered underground plant growth. The caverns have the underground creatures that pits, chasms, and underground rivers did in 40d, have subterranean water sources most of the time, and trigger underground plants' growth, and are actually present on every map, and are thus much better. Wagons are somewhat redundant; they increased a caravan's trade capacity, but since item weights have been greatly decreased and pack animal capacities increased, they wouldn't much help now. In short, the only really important thing that's missing in 31.25 is the dungeon master, and that only isn't present due to a persistent bug.
The best version is the most recent stable one, in other words. In the past, the stable versions have typically been even-numbered, but due to the large number of changes with version 31.19, several bugfix versions came out in fairly rapid succession and as a result 31.25 is the most recent stable version.