Printing out web content is a big no no. Potential employers aren't going to be very impressed with screenshot. And in fact, doing that may cost you some points with your interviewers. You're supposed to be showing them animation and interactive websites, not what they look like on paper.
For that type of media, put it on a CD.
If you include a website though, make sure it works. You may be saying "duh" but what most new designers don't know is that a website that works in Safari might have coding conflicts with Firefox, or Mozilla, or Internet Explorer, and may display differently than what you saw on your computer. You don't know what internet browser the person looking at your portfolio might have so you want to make sure it works on ALL browsers. If it doesn't, then it's a big red flag to them that you don't know what you're doing.
http://validator.w3.org is a site that will check you html code validation over different browsers.
With animation, don't assume your interviewer has a Flash Player. Sounds insane, I know, but often times, before your portfolio goes to be reviewed by the "creative people" with the "creative software", your portfolio may first be looked over by basic Human Resources administrator who doesn't have or need the programs that can play your animation. So for the sake of compatibility, convert your .FLA or .SWF into a Quicktime .MOV since most computers support this type of file and your animation will still play as normal.
Now, you might not even need those things anyway. What you put in your portfolio depends on the job you are applying for. If you sent a website and animation to a place that does mostly print design, they wont care much about your web based skills. And for that matter, any web based work that a company does is done by a graphic designer who specializes in web design. That doesn't sound like your area of expertise.
One thing you're missing in your portfolio is a piece that is text heavy. Some like a newsletter. You're employer will definitely want to see that you have a strong sense of typography with ALL varieties and amounts of text. A website is a good way to show this too, but it's really up to you which way you want to go.
That's all I got now but mattymjb@yahoo.com if you have anymore questions.