In addition to open requests (e.g. search for label color, add multiple labels at once), it would be great if the feature could be enhanced in general. For example, it would be great to associate a color with a certain folder and also allow multiple tags per entry. E.g. you have a folder about DIsease X (color red) and another at the same level about a technology or a gene of interest (color yellow). You could then easily see that a folder with a red and yellow dot belongs to both folders.
This would make the organisation of data - thousands of items - so much easier.