mysql is garbage.
at one point it was faster than other "sql servers" because it did a lot of things wrong and didn't support a lot of useful features.
now it supports many of those features and is now a lot slower than other "sql servers".
heck, mysql is slower and buggier than sqlite.
mssql like most other sql servers will see the most performance boosts from better queries. the query analyzer can really help nail that down. if you're trying to tune for some vendor's application (where you don't control the queries) you should really ask the vendor what they recommend. "tuning" sql server in these situations is a good way to make sure you won't get support for their application in the future.
such is the high price of proprietary software...