The MS issue comes up a LOT in the IS industry. The problem is that 5 or so years ago everyone and their dog went through the 'specialized school' system of getting their MCSE. It really watered down the cert. Most companies that actually care won't even look at a guy that just finished a MCSE cert program. Now if you have years of experience along with the cert, then it's a whole other ballgame. Honestly, the CCNA Cisco cert is getting the same way. It's not as bad as the MCSE deal yet, but it's getting there.
Just think about what section of the IS industry you want to concentrate on the most and go from there. If you want to go into network infrastructure, then skip the MS stuff and go with Cisco. The CCNA is a good basic starting point as it is so easy to pass. Then move on from there. Getting a CCNE is a great goal, but Cisco still limits how many CCNE certs there can be. They don't want it watered down like the MS thing.
The most important thing you can do, though, is get experience. Experience counts for more than the certs in the real world.
Piling up certs won't hurt you, they just cost money and you need to decide for yourself if it will be worth it.