Several reasons come to mind including to reduce the volume to get a desired gravity and when using a malt loaded with a DMS percuser (sp) like pilsner malt, the 90 minute boil is helpful.
Perhaps it is used to make the final beer darker in colour.
Just some off the top of my head.
Almost forgot to mention getting more from your hops.
I've done 90 minute boils on many of my beers since going all grain. Partly to help get the final volume down near 5 gallons on some of my bigger beers or to help reduce DMS precursors when using a lot of pilsner malt.