Aside from aliasing and links, is there an easy way in Linux to tag commonly used directories and to navigate to a commonly used directory from the terminal.

To be clear the disadvantages I see with alternative approaches, and why I want a bookmark/favorites like system:

alias
Cons:
Too specific (every new favorite requires a new alias...although you could in theory make an alias that echo append your dir as a new alias, which would be sort of clever). Can't nest favorites in folders (can't think of a simple solution to this outside of heavy config scripting).

links
Cons:
Clutter directory make ls a headache.

pushd/popd
Cons:
Non-permanent (without shell config file scripting), can't nest favorites in directories, etc.

Granted I have multiple ideas for making my own non-standard solution, but before I have at it I wanted to get some perspective on what's out there and if there is nothing, what is a recommended approach.

Does anyone know of such a favorites/bookmark-like terminal solution?