I'll give this a go.
"Dubbed" is generally as neutral as "called" or "named" in most usage. But it's exceptions are subtle. It's commonly used in identifying material objects or basically factual concepts, as in "Microsoft's media player dubbed Zune" - "NASA's next-gen launch vehicles dubbed Ares" - "Gatlin wins 100m race, dubbed fastest man". You are perfectly safe using it when your intent is clear. In fact, in these instances "dubbed" improves upon "named" or "called" by suggesting authority rather than hearsay.
However, "dubbed", as you've noticed, can reinforce a tilt toward scorn if that is your intent. Other recent headlines such as "stem cell research dubbed Orwellian" or "This handy list of tips will help you avoid being dubbed a spammer" use the verb pretty effectively to reinforce a negative tone.
"Dubbed" also carries a taint of sarcasm from an association with badly dubbed film and controversially dubbed vocal perfomances in popular culture. Children are often first acquainted with the word in a silly Arthurian pantomime where one, anoiting the kneeling other with a make-believe sword, intones "I dub thee..." whatever fun name comes to mind. This just leads to giggling... not an auspicious beginning for any word I suppose.