It really depends on the size of the database, the software systems already in place in your operation, plus the reporting requirements and functionality of the database.
Do you already have either of the vendors systems in place in your business operation, then stick with that one.
If the database is large (+200GB, or is forecast to be before 3yrs) and has lots of users, then go for MySQL as it is more scaleable.
If the database is smaller and has less users then use SQL Server.
If you will have to setup data loading (as in a datawarehouse) then SQL Server has a set of tools known as sql server integration tools which are very useful. Also comes with reporting services (allows you to publish intranet based reports very quickly) and business analysis tools to do OLAP.
The other choice is your server OS, MSSS limits you to MS OSs, My SQL will allow you more choice in server OS.
To review, if your users would benefit from you being able to tweak and configure to the nth degree because of the large scale of the data, large user base and dynamic nature of the data ... MySQL
If this is not so then you would benefit from the simplicity of MSSS in that there is much less that you as a DBA can do wrong.
Its not what is under the hood, it is what you need it for.