The Microsoft certifications are mostly a way to make sure that at some point certain thoughts have sluiced through your brain. That said, if you do a lot of Microsoft development this is not necessarily a bad thing, because it ensures that you've been exposed at least once to the 'right way to do things'. An MCP in whatever grabs your interest or an MCPD to show that you're serious isn't a bad idea if you do Windows development.
Sun Certified Java Programmer demonstrates that you know Java syntax. Sun's Certified Developer demonstrates that you know the libraries. Both are easy enough to complete and ensure that you've rounded out your understanding. A Sun Certified Enterprise Architect opens doors, but be prepared to work for it and you'd better really love Java.
ISC^2's CISSP serves as a good introduction to security principles and I think teaches the right model for how to think about security -- as a system of layers and controls, not magic pixie dust.
CompTIA's Security+ is a nice set of training wheels on the path to ISC^2's CISSP. If you are going to complete the CISSP, you might as well grab the Security+ on the way. You can even use it towards some of the Microsoft certifications.
To be honest, I used certifications to demonstrate knowledge until I had a graduate degree under my belt; I went back to college after the dot-com crash. But between that and 15 years in the field, no one really cares about my certifications any more.
So for me, they served as a great proxy for a degree until I had one, but I can't say that I've broken anywhere close to even on the huge pile of certifications I've accumulated.