Well more than software, websites, or templates what you need is a solid foundation of ideas of what you want to do and how you're going to accomplish it, along with a solid core of people. A rpg without other people defeats the purpose.
I will say that a good half of trek rpgs that crop up over the years don't get off the ground because of a lack of vision and primarily the creator just wants to be the captain. A lot of people do want to be the captain after all, it is human nature to aim for the top.
A commanding officer does need great people skills, organizational skills, patience and an imagination. Coming up with new missions on a regular basis alone is no mean feat for example.
Whether it's the big chair or a new vision you're aiming for however, the best way to accomplish this is often by joining an existing sim fleet where you can network with new members to possibly join yours, or earn your shot at the big chair from the bottom up.
Trek rpgers are a rather tight knit clique and I will say often the worst thing you can do for a sim is to go on other people's sites and message boards randomly advertising your own. Establish a reputation as a quality guy who contributes to the rpgverse however and you can get away with it.
I wish you luck with your endeavors, and if it would help you I can link you to a sim I participate in with a number of people, that you'd get out of it what you contribute to it.