Real Tone Records as said above,
My love is underground,
Sushitech - One of my favorites right now!
Strenght Music - DJ Qu's label
Live at Robert Johnson,
Innervisions - Another favorite of mine. Dixons label.
Delsin - Another Fave.
Uncanny Valley - Another fave
I really don't recommend using the beatport top 100. Its not really a good indication of what is best, just most popular. Unless that's what your looking for. But if you look out for charts by your favorite artists and then find labels from those tracks.
Pets recordings, Tsuba, VIVa music limited, Keinemusik, Hypercolour, Crosstown REbels, Hot natured, Noir Music, some of Dirtybirds releases, Ovum recordings, GEt physical music, Moon harbour recordings, Desolat, 2020vision, Off recordings, One records, no.19 records, the new saved release has some deep house...it really all depends on what kind of deep house you want really these are just a few off the top of my head but exploration is always the best way.
Open Bar Music
Poker Flat Recordings
Afro Rebel Music
Deeper Shades Recordings
Maurice Joshua Digital