You may have read the post where I mentioned using the LoseIt program when I first started trying to control my input and output. So why did I switch from LoseIt to My Fitness Pal (MFP)? The primary reason is that I started using Garmin devices which do not connect (or sync) to LoseIt but they do connect/sync with MFP.
I believe there are several features with LoseIt that I prefer. In general the two apps have similar features for nutrition and exercise tracking. MFP has more ads to deal with, but works great as a free program.
If your not using a device or not using a Garmin, I would start with LoseIt.