Yes, it's too late, at least in the US.
All the PhD programs I'm familiar with (mostly in North America, but a few European programs too) require admitted applicants to accept or decline admission offers by April 15. The admission offers themselves are sent out weeks or even months earlier. For example, my department tries to finalize all PhD admission offers by mid-February. We get about 750 PhD applications every year, so to keep ourselves (relatively) sane, we don't even consider applications that arrive after the December deadline.
A few PhD programs do consider applicants for admission in the spring semester. But I wouldn't recommend trying for spring admissions to the same programs that already turned you down. In my experience, spring admission is more competitive. Moreover, a few months is unlikely to significantly improve your application, especially since they've already formed an opinion.
I also agree with Joanna's recommendation: Your best bet is to strengthen your record and apply again next year, for admission in Fall 2013. If possible, get involved in a research project with the goal of publication. At a minimum, do something independent, creative, and technical to show off your potential for research. Show your complete application to your letter writers (or other faculty mentors), especially your research statement, and ask for their detailed and brutally honest feedback. Listen to them. Finally, confirm with your references (by asking them directly) that they are willing to write you strong letters emphasizing your research potential.