Although there are differences between the Allez and Secteur lines, and they are important, the differences are fairly subtle and specific to the intent of ride of each bike. They are both race/competition bikes. The Allez was designed to be, primarily, a quick and nimble race bike. Think of it as a "pocket rocket". The newer Allez borrows heavily from trickle down technology from the top of the line Tarmacs. It has a shorter wheel base, shorter head tube, stiffer forks, and fractionally more aggressive riding profile that makes it both fast and very nimble at short distances. The Secteur, on the other hand, is a new 2010 lineup introduction by Specialized meant to replace the Sequoia, and was designed to be a more inexpensive version of the Roubaix. As such, it borrows heavily from the Roubaix lineup technology. It is also a racing bike, but with endurance in mind, (longer distances). It has a longer wheel base, slightly taller head tube, zert inserts in the carbon forks to smooth out vibrations at longer distances, and a fractionally more relaxed riding profile.

Which one is best for you depends on your intent for riding and fit level. Each line has it's own trade offs, but at the risk of over-generalizing, shorter intense rides where you can sacrifice some comfort, the Allez may be your best choice. Longer less intense rides where comfort plays more of a role, the Secteur may be more your cup-a-tea.