Malaysia / Singapore / Brunei

A few thoughts:
Given the time commitment involved just getting there and back you'd be well advised to try to extend your visit as much as you can.
It's usually a little easier to get to Singapore from San Fransisco than it is getting to Kuala Lumpur - I know that SingAir has non-stop flights, whereas getting to KL will require enroute stops along the way. That said, broaden your search for airfares to include a multi city (open jaw) trip flying into one city and out of the other as well as round trip non stops to Singapore alone. The multi city routing would at least preclude your having to backtrack one day just to catch your return flight.
It's really not possible to visit Brunei from KL as a day trip - it's about a 2.5 hr flight each way - so you should plan on at least one overnight to maximize your sightseeing possibilities.
You don't say what your specific interests are, but a good place to look for day trip excursions is the Trip Advisor pull down menu for "Things to do" in each location. There's plenty to keep you busy in Singapore and KL, and Brunei has some very affordable package deals that might be of interest. Do try to get out of the city while you're in Kuala Lumpur. There are a host of day trip excursions that will take you out into the surrounding countryside, including (and recommended) trips to Malacca and the Cameron Highlands where the tea plantations are located.
Know that it will be extremely hot and humid while you're there - plan to take it slow and easy the first few days until you have a chance to acclimate.
Some of your routing options will include a stopover in Hong Kong. Depending upon your available time and personal interest you could layover there for a day or two to see one of the most fascinating cities in Asia, with the possibility of side trips to Macau and Shenzhen just across the border in mainland China. It requires a visa, which you can get upon arrival at the airport in HK.

We spent five days in Singapore as well as taking a three day tour of Malaysia that included Kuala Lumpur.

We loved Singapore. Malaysia was good, but didn't know our socks off.

As noted above, Brunei does note let itself to a day trip from KL. The good thing is that Air Asia has cheap flights from KL (make sure you get to the right terminal) - or at least they did when I did this route about 5-6 years ago.