Here's the scenario:
The party is in a rubble-strewn area, basically within an old building collapse. I've ruled that, for ranged attacks, they get 1/2 cover unless they intentionally state they are trying to find better cover, while they're in this area (or decide to climb to the top of the rubble, thereby losing their cover).
Enemy caster casts thunderwave in the middle of the rubble-filled area.
Here's the deal: cover helps with DX saves. Thunderwave uses a CN save. Yet is seems unfair to say that "cover doesn't help". This is stone rubble that's providing the cover, it should grant some benefit, wouldn't you think?
To not think so would suggest that thunderwave can pass through rock. There's nothing in the spell description suggesting that it does or does not pass through solid objects, but it is only a 1st level spell.
Would granting the +2 half-cover save bonus to a thunderwave's save bonus be fair, or too lenient?
I'd totally roll with cover providing bonuses to any relevant save, though I don't think a blanket rule would apply. Thunderwave and Shatter yes, Stinking Cloud, No.
Since the damage type is thunder (sound) and the characters only have half cover (i.e. their ears are not covered or protected) I would not go with any modification. It's like a wave of thunder (spell name) rolls over the rubble, not through it, and affects those cowering/sheltering in it. If I was convinced by a player that their enjoyment and immersion was going to be negated by my decision, I would apply the half damage modifier (+2) to the save as it's not a game-breaker for me.
Total cover would of course block thunderwave, like most other effects.
I don't really see partial cover having much effect on a blast of sound, so I would play it straight here. Actually, if you're in a rubble strewn area, I might be tempted to say the spell hurls a bunch of rubble at you along with the sound, and give you a little extra bludgeoning damage as well 
1. Thunderwave is not sound. It's "a wave of thunderous force" which deals thunder damage.
2. Thunderwave, unlike Fireball, does not "go around cover" or like the cleric cantrip Sacred Flame does not state "the target gains no benefit from cover for this saving throw."
Ergo, the target can benefit from cover if any. HOWEVER, the saving throw is a CONSTITUTION save. Cover only grants bonuses to AC and REFLEX defenses outside of course of total cover but hat's another situation entirely. So even though the target does gain bonuses from cover if any, it does not affect Thunderwave's saving throw.
It deals thunder damage as per the spell description.
Thunder damage: PHB p. 196 "a concussive burst of sound" and thunderwave is specifically cited.
Thanks for all the replies, everyone.