You are going to be so close so definately visit Machu Picchu and sites in the Sacred Valley such as Pisac (market and ruins) , the town of Ollantaytambo and its fortress , as well as Maras and Moray. The loads of little ruins between Cusco and Pisac and dont miss out on Sacsayhuaman which is in the hills above Cusco. Theres the Souther Valley sites of Piquillacta and Tipon as well and tours usually include the church at Andahualillas.
You could make a quick trip to Lake Titicaca but you need to plan for at least 3 days for Lake Titicaca...one day of travel to, at least one day to tour, and another travel day back. The boat tours depart quite early in the morning so unless you find an overnight bus it wont matter the mode of transportation you use, you will most likely arrive to late to tour the lake that day. The tour all return to Puno around 5-6PM so again unless you find a late bus or flight you will have to plan a second night in Puno and plan to travel the day after. If you are headed to Lake Titicaca after Cusco you may want to consider flying back to Lima from Juliaca insted of returning to Cusco and then flying back to Lima.