I applied to a computer science PhD program and received an email saying the department admissions committee has recommended me for acceptance to the program. What does it mean "recommended"? Isn't it the department making the decision?
Not always. At some universities (such as the one where I presently work, the official decision to admit a student is made at the dean's level, rather than the departmental level. In such cases, the department recommends admission; such recommendations are almost always accepted, unless something irregular has happened in the admissions process.
Yes, what aeismail said is correct. The recommendation for admission means that the department has judged you an eligible candidate, and they are recommending your acceptance to the level that makes the final acceptance (Dean/Admissions Office etc. depending on the context). I've never heard of anyone not being accepted after receiving a recommendation of acceptance.