San Ramon and Pleasanton have great schools and correspondingly high home prices/ lease. Dublin is nice to live in IMHO but I'm not certain about the schools. It would help to know what range you're looking at.
Mountain House, Tracy and some areas in Livermore are much more affordable but the commute to SF might soon become tiring not to mention wear/tear on vehicle, gas prices etc.
Cupertino and Palo Alto are other great areas for schools but again, you're looking at more expensive home prices. A friend rents a modest sized home in Cupertino for $3500 and another friend for $4000-ish. Sunnyvale is popular and less expensive, and I am not too sure about schools...you'd have to do a bit of research. With immigration of local and foreign computer professionals there are many apartment communities in San Jose, Santa Clara, Milpitas, Sunnyvale, Cupertino etc that may be more affordable. Good ones are about $2300/mth for a 2-room. Community pools, clubhouses etc are included.
I personally favor Fremont for its convenient location. Again, not certain about schools but we homeschool so schools are not an issue for us. Berkeley area is another good bet but I'm not certain about home prices.
Do narrow down a locale if you can and hopefully I'll be able to suggest more options.