Make your set list. Your set list should have a comprehensive order. Topics should be in a sequence and have seamless transition that makes sense so that it will appear that you are having one long conversation.
Use your improv skills. Longer sets are a good chance to work on your jokes a bit. Improvise, and try to have fun with your jokes. Tell the longer version of your stories and make sure to take notes after your set, so you can see what went over well with the crowd and what didn't. This is a great way to hone in your skills.
Work the crowd. You have the opportunity to talk to the crowd. Have conversations with them. Feel free to really let your creativity run wild, and don't be too worried about running back to your set. An audience loves crowd work and if you are on a tight time schedule, you can always cut out some jokes. Typically though, this will just help your set to flow.
Tell stories. Feel free to incorporate stories into your set as well. Long sets don't always need to be joke after joke. Tell personal stories that you think are relevant and humorous.
Keep track of your time. Even if you have a long set, make sure it doesn't go overlong. Always end when you are on top. Get your big laugh towards the end of your set and leave them wanting more.