dark labels that come to mind are subtitles, black sun empire, renegade hardware, moving shadow, metalheadz, tech itch, virus, freak, obscene, shadow law, hostile, and barcode. moving shadow caters to both lighter and darker stuff but it's all classic. check tarzan and find some producers you like. see what labels they've appeared on so you can start building a list of labels you like.
dark/intelligent i'd recommend offshore and reinforced.
If you want it to be more intelligent dark rather than dancefloor orientated check out labels like Offshore they've got some wicked limited edition 10"'s floating around, Moving Shadow as Organix said, & I would say Eastside's older tunes are worth ago. Also Alpha Omega does tracks like this.