Wouldn't you be expected to produce something more "masterly" as your masters level thesis ?
Since you already did a comparision of two web site development technologies for your bachelors degree,
you should be in a position to do something a bit more complex.
Your choice may also be driven by what your University expects and approves as a topic. You may be constrained by the subtle differences between computer science, computer engineering and computer applications.
Off the top of my head:
Computer Science Related Topics:
a) Something related to SOA and webservices
b) Something related to Grid computing
c) Something related to p2p / agent based computing
Computer Engineering Related Topics:
a) Challenges of Geographically Distributed software development
b) Levaraging Open Source software in the real world
c) Governance and Architecture around SOA