From recent design projects I was quite impressed by the task manager produkteev. This tool helped me to stay in contact with everyone involved and always gave me a great overview of my recent changes and upcoming tasks. I also decided to use it as a tool for managing my research work.
This tool provides four information layers: Network, People, Projects and Labels. Network describes the overall project structure that I am working on a daily basis. Working with different partners and clients I need to have them all in one place but visually divided. The next layer provides an overview over all the people that are involved working with you on a certain network. Probably one of the most important layer is the project layer. There you add projects to the network - since this can work as a pre-task list it can get quite confusing. Tasks are INSIDE projects. Which I would describe as a sublayer to the project layer.
Alright! Another important feature (if not the most important) are the labels. Use as many labels you want. This comes handy when a project blows up very fast and you'll need to look for this special little detail. Using labels makes working productively much faster and easier.
Of course this tool has countless other features like search, filter, priority, etc.
To round up this post; there are many other task management tools in the wild. I decided to stick with produkteev since I already have some good experience with it. Let's see if this will work for research work as well.