Staying in Sunnyvale, visiting San Francisco 1 day. Which transport pass?

This is unanswerable without knowing how much you'll use each mode of transport, and how far you'll go each time.

Clipper is usable on BART, MUNI, and Caltrain. That sounds pretty convenient.

Having a Clipper card would be convenient, as it can be used on BART, CalTrain, and MUNI. In your sort-duration trip, however, obtaining a Clipper card may be more trouble than it’s worth. The challenge is that while value can be easily added to a Clipper card in many locations, the card itself is harder to obtain.

Some BART stations have humans in a ticket booth (SFO and Millbrae are like this), and all BART stations have ticket machines. These booths and machines will sell and dispense BART cards, and can be used to add value to BART cards and to Clipper cards. These locations, however, do not offer the Clipper cards themselves.

You can order a Clipper card by mail, but the Clipper ordering web page doesn’t address shipping to international addresses. If you have time before your trip, you could ask Clipper Customer Service by telephone or webmail.

Clipper cards can be purchased in person at several locations in downtown SF and San Jose. The Sunnyvale CalTrain station is not listed on the Clipper card map of places to buy a Clipper card; I conclude that the station is not staffed and no card sales occur there.The closest buy-a-card locations to Sunnyvale are the two Walgreens locations: 1306 South Mary Avenue, and 105 East El Camino Real.

The Sunnyvale CalTrain station is a bit over 1 km from the Walgreens at 105 East El Camino Real, a 15 or 20 minute walk. With only one day to explore the area, you may decide that the one-hour sidetrip to Walgreens in Sunnyvale takes too much time.

Without a Clipper card in hand when you arrive at SFO, you’ll have to buy a BART card at SFO to travel to Millbrae, then buy a CalTrain fare at Millbrae for your trip to Sunnyvale.

All in all, you may prefer to buy individual fares or cards for each system (BART, MUNI, and CalTrain) as you use them. Were this my trip, I’d probably do that.

EDIT: I was incorrect in asserting above that Clipper cards aren't available at BART stations. This current BART page says:

Automatic Ticket and Clipper Vending Machines

Most BART stations sell tickets and Clipper cards through automatic vending machines that accept nickels, dimes, quarters and $1 coins, as well as $1, $5, $10 and $20 bills. There is a one-time $3 per card purchase charge from Clipper. Credit and debit cards may be used at all stations in select machines.

...

In Summer of 2019, BART started a pilot program that expanded the number of stations where the only fare product available for purchase is the Clipper card. Stations without ticket vending machines include Embarcadero, Powell Street, 19th Street, Downtown Berkeley, Pittsburg Center and Antioch.

(I think the last sentence lists stations where no BART cards are sold...but I'm not sure.)

Caltrain is terribly slow, so it will take you an hour to ride from Sunnyvale to San Francisco. Evening service is quite limited, and takes even longer (1h20). Be sure to check the schedules before you leave, and plan your day.

If you can't get a Clipper Card beforehand, it'll cost you $16.50 for the return trip between Sunnyvale and San Francisco.

In San Francisco, you just need Muni, which will cover buses and trams. The simplest option is probably to buy a Day Pass on the Muni Mobile app ($5).

Note that this does not include cable car rides (which are now $8!). You can either buy those separately within the app, or buy a 1-Day visitor pass ($13) in the app, which gives you access to all the same things as the Day Pass, but also includes cable car rides.

Note that there can be very, very, very long waits for cable cars, and the historic streetcars can also sometimes have a bit of a wait. Don't forget to factor that into your schedule.

Unfortunately, as you've noticed by now, the Bay Area is a mess of different transit agencies that don't really care for each other and don't have a whole lot of regard for the practicality of the rider experience. While there are efforts to improve that situation, it presents some problems for your trip.

The good news is that the BART station at SFO now has a machine that vends Clipper cards. Look for it at the airport BART station next to the faregates. So if you get to the station after you arrive, you can buy your card, load it up with cash/debit/credit card, and take the train the short and expensive hop to Millbrae (there's also a cheaper bus that does the same trip, though the schedule varies).

BART clipper vending machine at sfo

From Millbrae, transfer to Caltrain and pay with the cash balance on your card (no pass makes sense for this unless you'll be stopping off places along the way). Do the same for your Caltrain trip to/from SF on Saturday. Be sure to check the Caltrain schedules, as it runs irregularly outside of commute hours and there are only a couple of trains at night. When you ride BART, there are faregates where you'll tap your Clipper card in/out. However, Caltrain just has open platforms, but there are sometimes-hard-to-find card readers placed along them. You must tap your card before you get on the train and after you get off. If you don't do the former, you can be fined, and if you don't do the latter, you'll be overcharged.

However, and this is where it gets "fun," Caltrain is not running to San Francisco on weekends for the next month due to construction work for an electrification project. There will be free buses at the Bayshore station that will take you the rest of the way, but this will add significant time to an already lengthy journey. The best option depends on where you want to start your visit to SF, as the area near the SF Caltrain station isn't the most touristy. It will cost a little more and will still take a while, but I'd consider getting off Caltrain at Millbrae and taking BART into San Francisco; you could go to Powell Station to visit Union Square and proceed into Chinatown, for example, or get off at one of the Mission stations and walk and explore the Mission District, or transfer to Muni and go to the Castro, lots of possibilities. You'll need to reverse the process to get back, keeping in mind the Caltrain schedule.

Another option, which is a little unusual for a tourist but might make sense with the construction, is to get off Caltrain at Bayshore where it terminates, but take Muni's 8-Bayshore bus all the way into San Francisco, as it crosses the city and can take you near Chinatown, North Beach, and Fisherman's Wharf.

Within San Francisco, you have lots of options:

• Muni day pass ($5). You'd think you could just load this on your Clipper card, but that would be logical and convenient, so instead you'll need the MuniMobile app. Good for unlimited rides on Muni, which includes buses, the Muni Metro subway, and historic streetcars; does not include cable cars (see jcaron's excellent answer for more on that).
• Muni 1-day passport ($13). Get this if you want to take at least one cable car ride in addition to other Muni trips. You can get it loaded onto your CLipper card, but it's probably easiest just to buy it with the MuniMobile app.
• Single-ride fares ($2.50 with Clipper). Tap your card when you get on a bus (no need to tap off with Muni) and pay out of your Clipper cash balance. Despite the name, the fare is valid for 2 hours. The day pass makes more sense unless you're just going to take one ride.
• Other forms of transportation: walking, bike share, more bike share, rental bikes, scooters, Lyft, Uber, taxis. I recommend Google Maps and the Transit app to help make sense of the options and realtime information about when buses are coming.

Lastly, if you're traveling in a group to/from the airport with at least one other person, you can use the BART to Airport app instead of a Clipper card for a special discount on BART fares for airport trips only.