Absolutely include any 3d work you have already done, unless it's fanart (they hate that in portfolios). They won't mind what softwares you've used so far, as long as they can see you have potential. I'm going to be doing animation in Septemer, but mine is 2d, so it required a few different things, like traditional work, however I think it would still be good to include some life studies, like human figures, in any medium, because it shows that you can work from different perspectives. Which uni are you thinking of applying to, because it's different for each one. Also character designs are an absolute must so definitely include that.