Hey mate,
I'm old school, so I often put together a set of hard copy clips. When it comes to stuff that appeared online, I'll usually just print out the web page, unless it is hopelessly cluttered with ads and such. In that case, I'd copy and paste into a word document.
In recent years, I've gone to sending clips electronically more often. Seems like more and more people prefer that, so fine. I have a set of files, each with various stories, that I can add as an attachment to an email. The files aren't too large, so that's not a problem. I used to worry about whether the person on the receiving end would have the necessary software to open the attachment, but that hasn't been a problem thus far.
Whatever format you choose, WHAT you send is far more important than the method you use to send it. For most positions, I try to include a mix of event stories, breaking news, enterprise, features and columns. If I know the details of a particular position (college beat, hockey, golf, whatever), then I'll often pick clips from that sport.
I should say I've been out of school for more than 20 years and have hundreds of clips to pick from. When I was just graduating, I'd send whatever I had that looked good: college paper, internship, games that I freelanced, anything that showed I could write nice and tight.
Best of luck in your search.