Parapat is connected to Tomok and Tuk Tuk on the Samosir Island by a ferry that runs every hour for Rp 15,000 (motorbikes Rp10,000 extra, as of March 2015), running on the half-hour except the last one at 19:00. The place to catch the ferry to Tuk Tuk is called "Tiga Raja" harbour/jetty. The ferry man will drop you at the place you're staying at in Tuk Tuk. Try to use the ferry with a wooden bench inside and that's coloured light green. Those are the ferries that charge Rp 10,000 and that the locals take to cross over. Tuk Tuk is the main town to stay on Samosir. Use the boat service not the large ferry, they will drop you directly at your Tuk Tuk resort.
There is no point to go to Tomok as there is no accommodation there. There are tens of guesthouses in Tuk-Tuk.
Return trips leave from various places in Tuk Tuk on the hour, but sometimes 15 minutes earlier/later. Wave down the ferry to ensure it comes to your dock.
There is also a car/passenger ferry at Ajibata, a very short distance south from Tiga Raja.
The ferry ride over is fantastic, just truly peaceful, apart from the car radios playing, the ladies selling peanuts, bottled water, noodles or pretty much anything else. Normally some of the passengers and vendors will be able to speak English. Landing at the other end of the 1 hour ferry journey is daunting, but again, behave like everyone else in Indonesia and just push, ever so politely, but firmly and eventually you will get off the ferry and onto the main road. Alternatively use the boat service but watch out for the guys that ask for the fee before you embark — they do not work for the operators, you pay on the boat.