There are two main types of negative carrier, with and without glass. There are arguments for and against each type. Lets be honest there are three types, the adjustable.
Glassless carriers avoid the Newton rings effect (a post for a later date) but also have the disadvantage of allowing the negative to buckle when they warm up, this is more pronounced with 6x6 negatives. To minimize this you should be very careful when focusing and use a smaller aperture to increase the sharpness across the negative.
Another disadvantage of a glass carrier is dust; to be honest it is not the big deal that everyone makes it out to be. It is just a case of being methodical in your approach. The main advantage of glass carriers is that they keep the negative flat. Another plus is that you can experiment with unusual effects by using various materials such as flower petals, salt crystals and soap suds etc in the carrier.
There are adjustable carriers also, which are very handy as they allow you to mask out badly illuminated edges without having to increase the magnification, or you can adjust them to include the rebate of the negative.