BART is being extended southward, into the Warm Springs District of southern Fremont, and from there to San Jose.
BART - Warm Springs Extension Project
BART to Silicon Valley - Santa Clara Valley Transportation Authority
Berryessa Extension Project (PDF)
The 5.4-mile Warm Springs Extension is now under construction, and it should be finished by 2014. The 10-mile Berryessa Extension should start construction in 2012, and it may be done by 2018 or 2019. Santa Clara County officials put off the rest of the San Jose extension (about 6 mi) from lack of money, though they are still planning it.
It will go the Fremont station on an embankment into some vacant lots, where it will descend into a cut-and-cover tunnel. This tunnel will go under Stevenson Blvd. and Fremont Central Part, including the northeast lobe of Lake Elizabeth. It then will go under the ex-SP/ex-WP UP line and surfaces a little north of Paseo Padre Pkwy. It then will parallel to the UP line the rest of the way. The foundations for a future Irvington station will be built just south of Washington Blvd., and the Warm Springs station will be built just south of Grimmer Blvd.
From there, the line will continue parallel to the UP line, and south of Abel St., it will follow the east, ex-WP UP line. Its Milpitas station will be between Montague Expwy. and Capitol Blvd., near the Montague light-rail station. The Berryessa station will be between Berryessa Rd. and Mabury Rd.
Judging from the published maps, the line will go into a tunnel and follow Hwy. 101 (Bayshore Fwy.) to Alum Rock Ave., having a station there. It will then turn westward underneath Santa Clara St, having a station underneath the 1st/2nd-St. light-rail station. It will have a station at the Rod Diridon station / HP Pavilion, and then go north under the Caltrain line, having a station at Caltrain's Santa Clara station.
There's a nice slideshow of construction pictures at Construction Updates page. A temporary dam has been constructed to permit the construction of the BART tunnel under Lake Elizabeth; the water has been pumped out of the northeast lobe. Some parts are further along; the Fremont Dog Park has been restored.