Personally, I'd take the southern route too. However, abenz still needs to avoid commute traffic. Although I mentioned avoiding the southbound morning commute on I-680, northbound I-680 to Fremont is equally bad, as is I-880. I speak as someone who commuted to two companies in Fremont from the southwest and from the north over a number of years.
I used to joke that it was "easier for me to go to Singapore than to go to the office"; A limo would pick me up at home (so I didn't have to drive), get to SFO and sit in the Biz or 1st Class lounge, have a comfy seat (or sleeper) for 18-20 hours, sleep/eat as I wished, and arrive "fresh". OTOH on the "parking lot" (the commute) I'd watch people eat their breakfast, brush their teeth, put on their makeup, read the newspaper, do crossword puzzles, talk on their cell phone, get mad with everyone around them, and more.
Nowadays, I avoid the Santa Clara Valley (aka Silicon Valley) like the plague; There's just too much traffic, and "commute hour" lasts 4-5 hours.
I'm still curious to read JCZ's "... into Fremont the back way, avoiding all the Bay Area traffic". I don't know any way into Fremont during commute hours that avoids traffic.