I have used Tripit (free), Kayak, and Tripcase.

Tripit (free) - no alerts
Kayak - I like that's clean interface, free alerts, sometimes baggage information, pretty instant notification on gate changes, flight changes
Tripcase - pretty much similar to Kayak, but I felt that tripcase was always delayed in sending flight change notifications. I believe Tripcase uses worldmate services to provide alerts.

For me winner is Kayak