Aha interesting that you posted that. I'd have to say the Route 216 night-time theme is one of my favourites, although I haven't played the games in years (not an exaggeration, other than reaching Sandgem Town with a Turtwig a few months ago, my last save started in 2012 - i checked the dates on my Froslass).
Route 216 night:
Likewise Canalave City (night-time)
This is probably the best outside-of-Pokémon-League music ever:
The Battle Tower music is far more enjoyable than the facility itself, and I think makes up for the fact that unlike the Emerald one it doesn't let you clone your Pokémon:
Not one of my favourites but I find night-time Pokémon Centre to be the only time the Pokémon Centre music doesn't grate on me. I think it's because it actually fits the theme of them as places of rest, rather than being incessantly perky. Especially welcome when I ended up spending a lot of time in there trading back when the GTS etc. still worked.
I honestly think the music is one of the things Pokémon games do right, and having different night-time themes make DPPt stand out just a little. Given all my free time now is in what the pokémon games classify as night-time, its nice to have music that fits the time, sometimes I'm playing LeafGreen with only a lamp on and Cinnabar Island's theme even manages to seem too perky (even though its one of my all-time favourites across generations).
EDIT: Thought this was just for DPPt, I'll let some other people post before I spam this up with an essay on my favourite HeartGold / SoulSilver music/