I watched the film only recently and wanted to find this out myself and, handily, on the message boards on IMDB I noticed the above question. It was answered by "swlf63" ...
"Just as there are many thematic layers to the film itself there are several layers to the title:
*Magnolia Blvd. is a street in the San Fernando Valley where the film takes place. Some of the characters in the film I believe drive down this street.
*Magnolia sounds similar to "Magonia", a term created by Charles Fort (who wrote about strange phenomena and is referenced in the film's closing credits) which is an alleged place in the sky where things are kept until they fall from it.
*There is a legend that the bark of the Magnolia tree can cure cancer.
*A magnolia is a type of flower, which is used as a symbol throughout the film. The concept of the blooming flower has been used as an analogy for the film's structure and flow.
*Magnolia is an 8 letter word with 2 "a's", being the 2nd and 8th letters. This is an odd coincidence which relates back to the numbers 82 featured frequently in the film as a reference to Exodus 8:2: "If you do not let them go, I will send a plague of frogs."
I am going to buy the soundtrack and anyone who has not seen the film must watch it now.