It depends on why you want to get certified. If you are looking to impress an employer, then I would suggest doing neither and spend that time working on an open source project or your own project. Experience will always win out over certifications.
Thanks Mathew I have been doing Java since last 1.5 years (EJB)but looking at the current market I am really worried about my future. Do we have more java developer than required? Do we expect .Net boom next year?
If you really feel obligated to get a certification, I'd go for .NET for no other reason then because there are already tens of thousands of SCJ*'s. You'll stand out more in the next 6-24 months with a .NET certification. --Mark