I am recording this feeling since it doesn't come around all that often ;)
Seriously - I spend a lot of time wondering if I'm doing the right thing, if it's going anywhere, feeling lost and/or unsupported by my department, and/or trying to catch up with work I've missed through being ill. This is in addition to all the usual stresses on PhD students.
Right now, I feel as though I have a range of both short- and long-term goals, and I have some idea where I'm going. I trust Mark W, my new second supervisor, to be familiar with the current computational chemistry literature & am fairly confident that no one else has done what I'm trying to do. Several things I'm doing could independently make short journal articles if they work out.
It's kinda nice to have some self-confidence occasionally.