I've just started my phd(3 weeks ago) and my supervisor has planned a meeting for next week to decide how to move forward and design some experiments. I get along with my supervisor really well and what to be able to come up with some sort of useful input, but I'm worried that I wont have anything to say.

Just read the relevent papers and get some ideas from there. Also, a good way to start is to do something basic, whether its designing your own primers for PCR, making up reagents or doing simple microbiology propagation. Doing something simple and it working will boost your confidence. Its great you get on with your supervisor, just be honest with them if you are feeling a bit unsure (they too were once in your position).