date and time is the biggest the difference between the databases.SQL server 2005 has datetime (with microsecond) and smalldatetime(no microsecond) data type where as mysql has date, time, datetime and timestamp datatypes to handle date time components.
In mysql, if a blank value is inserted into datetime data type, it is stored as 0000-00-00 00:00:00 where as in sql server is stored as 1900-01-01 00:00:00.000. And if the application had been developed around mysql and logic in the application to handle the peculiarities with datetime in mysql will have to be thrown out of the window if the application needs to support sql server.
as mysql has no concept of microseconds where as sql server datetime has microseconds. If the application does not handle microsecond, the application will have to be rewritten to handle it.