I suppose it depends on what we consider to be "enhancing" the functionality of the packages. Thinking about packages which appear to be specifically directed to processing the output of these tools, the package Glimma comes to mind because it is focused on exploring the results of limma, edgeR, DESeq2 to produce interactive plots, so I guess it can be considered to enhance functionality. Or for example stageR or IHW which are used to do "post-analysis" of results outputted by e.g. limma or DESeq2.

It is no coincidence that many of those packages (e.g. Glimma or IHW) are created by developers of the original tools. So tools published by those groups are a good place to go looking for packages enhancing functionality, I guess. Workflow papers such as this one usually provide many examples of packages which are well integrated with the output of these tools.