The non commercial wads I play the most are:
Hacx (v1.2 is free now and packed as an iwad).
Phobos Anomaly Reborn (for DOOM 1).
The Darkening Episodes 1 and 2 (for DOOM 2).
The Brotherhood of Ruin (for DOOM 2).
Strain (for DOOM 2).
1024 Congestion (for DOOM 2).
There are also some wads that demo engine features. For example the Artic series demoed MBF features such as friendly enemies, fake water, crate puzzles, friction and more.