The first sort of connection is the taxonomy navigation which Drupal autogenerates. For each taxonomy term Drupal generates pages listing the node's which have that term. Each node lists its taxonomy terms as a link to that page, hence the reader will have an opportunity to immediately browse articles in related terms.
The Similar By Terms generates a block of article links which have similar taxonomy terms. This is triggered by the other nodes that have the common terms. The Related Links offers similar functionality, but works using the search engine rather than the taxonomy system. Installation of both is very simple, essentially you install the module and then enable the blocks it generates.
The directory module generates some fairly nice pages summarizing a given taxonomy. It lists all terms in the taxonomy along with a count of the nodes having that term. This should help the user more easily browse your taxonomy structure.
The Tagadelic module also generates a summary listing of taxonomy terms, but rather than showing it as a straight list the terms are shown in a tag cloud arrangement. Tag clouds are this newfangled web 2.0 idea which makes the text size show the relative importance of terms in the cloud. Supposedly this helps to browse terms by seeing the more important ones more quickly. The jury is out on this.
The Taxonomy Breadcrumb module works to improve the breadcrumb trail shown before a node. The breadcrumb trail is meant to be a map of how to navigate the site hierarchy to get to a given page. By default, when viewing a node, Drupal just shows 'Home' in the breadcrumb trail. It is desirable that the user to have better access to the related articles. The taxonomy breadcrumb shows the taxonomy hierarchy related to each node. It also allows the administrator to specify a page for each taxonomy, and a link to this page will be put in the breadcrumb trail.
The Synonyms module makes the related terms function in the search index. Each term can have a list of related words, or synonyms, and by default these are not findable through the search system. The synonyms module adds these words to the search index, making the content findable using those search terms.
The Taxonomy Query Language module is a cool-sounding idea, but I've not been able to figure it out. The idea is to have a simplified and more powerful way to query a vocabulary for interesting items. Using vocabularies for navigation discusses the out-of-the-box methods for selecting interesting lists of nodes based on the vocabulary terms. The core taxonomy system can generate a list of nodes having a specific term, or a list which is the intersection of two or more terms (AND), or a list which is the union of two or more terms (OR). TQL goes further allowing you a more general boolean expression to select interesting nodes. But as I said I've not been able to get this to work.