Hilton Garden Inn
1800 powell street, 510 658-9300, (http://hiltongardeninn.hi...). west of i80, close to the bay.
Four Points by Sheraton
Christie and powell. great location, decent hotel. has a "business center".
Woodfin Suites Hotel
5800 shellmound street. each suite has a full kitchen, living room, with separate bed & bath. bay views. situated between bay street and the emery bay public market. home to emery grille. reservations 888433-9042, direct 510601-5880, (http://www.woodfinsuites....)
Courtyard Oakland Emeryville
5555 shellmound street shellmound past christie, 510 652-8777, fax: 510 652-8799, (http://marriott.com/prope...). directly across the street from bay street shopping/eating and rooms facing the bay get a great view. modern and clean facilities.
Emeryville actually features many of the most modern hotels in the Berkeley/Emeryville/Oakland region. Thus, you may choose to stay in Emeryville while actually spending your days in the other more interesting cities.