In many ways, KDE's Dolphin and GNOME's Nautilus are similar in structure, with a directory tree on the left, and a pane for displaying the contents of the current folder beside it. Both, too, have the zooms and icon and details view that you would expect in a file manager, to which Nautilus adds the ability to add an additional emblem as a sort of tag (a feature I have yet to find a use for). Both, too, support tabs and additional panes.
However, Dolphin adds a pane on the right that gives detailed information about the currently selected file. This system is much handier than Nautilus' zoom feature, which gradually displays more information as you zoom in. You can choose in the preferences what files are displayed in this pane, in case the feature uses more memory than your machine can easily handle.
Dolphin also benefits from KDE's indexing of files by having an advanced search function that can search not only file names, but also file properties and content as well.
Some KDE users still prefer Konqueror to Dolphin. However, on the whole, Dolphin strikes a reasonable balance between simplicity and functionality. Nautilus, on the other hand, tends to err on the side of simplicity.
Both GNOME and KDE have taken some pains in the last few years to improve their document viewing. The results are Evince in GNOME, which displays PDF and image files, and Okular for documents and Gwenview for images in KDE.
The separation of documents and images can be confusing when you go to open a file and have to remember which viewer to user. Yet the wisdom of the separation soon becomes apparent when you compare Okular and Gwenview with Evince.
In trying to deal with two very different sets of requirements, Evince settles for a lowest common denominator approach, offering only basic features like zoom for both text and images. Nor can Evince handle Open Document Format, even though, being much small and quicker than LibreOffice, it would be a handier tool for quick glimpses of a file.
By comparison, the division between Okular and Gwenview allows for more specialization. Unlike Evince, Okular offers a PDF viewer that is a near-clone of Acrobat Reader. It includes features like text selection, as well as a set of review tools for highlighting text and adding bookmarks. You can even have a document read to you, if your system is set up for that.
Gwenview is similarly versatile, with basic editing abilities and the ability to import and export from online image collections. At the same time, the Gwenview window is as close to Okular's as possible, making it easy to move between them.
Like many IM tools, Empathy and Kopete display in small windows that minimally intrude upon the desktop. Both are suitable for messaging and file transfer, and Empathy has some limited used as an IRC client. Many of their differences are organizational rather than functional -- for example, you add a new account to Empathy via a wizard opened from Edit -> Accounts, while to do the same in Kopete, you open the configuration settings.
The main functional differences between the two are in the extra features. Empathy provides a separate window for previous conversations and file transfers, as well as the location of contacts on a world map, while Kopete provides a series of plugins for everything from Translation, rendering LaTeX formulas, encrypting, and adding notes about each contact.
Transmission is an app that has changed little in the last few years. It starts with a solemn warning that you alone are responsible for what you do with it, then opens on a blank screen that offers few hints about what you should do next. Everything about it assumes that you know what BitTorrent is, and how to go about using it.
KTorrent is at the opposite extreme. As with Transmission, users may be confused about what to do first, but, with KTorrent, the reason for their confusion is too many possibilities, rather than too few. Divided into three panes, with a menu bar on the left, KTorrent is a typical crowded KDE app.
Both Transmission and KTorrent are supported by clear, concise help files, but both could use a wizard or more hints in the interface about how to use them.