One of my major complains with Bay Area is about its public transport. I specially realized the problem as I have been renting a car on every time I was visiting but after I moved here the car renting looked too expensive to continue (~900 dollar a month).
I am happy to be have been proven wrong at least about San Francisco's public transport.
Finding the route options
So this morning I had to visit a office in San Francisco at 9:00 AM. I figured out ways of transport using Google Transit and SFMuni. Google Transit works well for figuring out route from point to point. As expected routing involved
1) Walking to Cal train Station
3) Bus in San Francisco to destination.
Google Transit takes arrive/depart time as an option and I could figure out the right options without looking at too many time tables.
SFMuni website came in handy however as unlike Caltrain the Muni has multiple alternative routes that you can use depending on how much you are willing to walk with a reasonable 1/2 mile walking option I got quite a few buses to choose from.
About the transport itself. Well Caltrain experience didn't start very well as it came about 25 minutes late and they asked us to switch platforms twice, but desptite that the train annoucements were helpful and they suggested that At Palo Alto station we can switch to the fast Mini Bullet Cal Train. Doing so we could easily make up for the delay and we did.
In San Francisco after getting down at Cal Train I could catch a single bus (I didn't follow the routing now as I learnt there were quite a few buses) to reach my destination. More interestingly the 2$ ticket issues was valid for next 4.5 hours, so I could use it for multiple return journeys, Muni train and Muni buses. AFAIK you can travel to almost all parts of the city using these two options.
Cost and Time
Overall I spent just 14$ for the round trip. One small point though, the Caltrains frequency varies from 30 minutes (before 11 AM and after 7 PM) to about 1 hour(11 AM to 7 PM), so your trip can get delayed if not planned well. Also it takes the slow train about 70 minutes from Mountain View Downtown to SF station, the faster (baby bullet) takes just 45 minutes.
Carrying bikes in Caltrain is easy, they have two kinds of coaches offering either 24 or 40 cycle carrying capacity. In both my trips the train has enough space for few more bikes. The caltrain stations have different facilities for parking bikes. In general you can easily carry around your bike in SF and lock it to one of the many on street bike lock stands.
In conclusion, SF's public transport is about as good at other cities I have been too, of course nothing beats a proper metro transport like that in Hong Kong, Paris, London and New Delhi*, but MUNI is SF can get you from one point to other and quite time efficiently.
* Didn't get a chance to explore New Delhi metro much but it looked great though it still doesn't have full coverage.