for all the terrible things about its planning and entitlement process, san francisco actually does a very good job preserving historic buildings and the districts they form together. there are a number of places in the city where tall buildings are woven into the fabric, in many cases supporting or enabling preservation that would otherwise be more financially difficult.
like new york, there are also ways to transfer air rights (TDRs here) which in essence compensate and the owners of historic buildings for the un-developability of their land.
it's most successful in the way that the high rises around union square, yerba buena gardens, and the western edge of the financial district blend into the very dense, bustling shopping and eating/drinking which is mostly accomodated in older mid-rise buildings. you also see it in smaller preservation districts throughout the city.
there are some important policy moves which allow this. the base floor area ratio of most downtown sites is actually fairly low. to increase it to skyscraper levels requires transferring development rights. there are exceptions, but generally no development rights can ever be transferred to a lot which contains or once contained a historic structure. even the newer districts which don't limit maximum floor area ratio generally preserve this basic method for increasing density beyond the mid-rise base.