The reason I favour some console applications over their graphical equivalents is that they're designed to be easy to use with a keyboard. A little while ago I wrote about a day I spent trying to perform my usual online and music-listening tasks using console applications, just for fun. These days I spend my time in KDE4 and have my graphical web browser back so that I can keep up with xkcd. I'm still using cmus to play my music and irssi is going to remain my IRC client of choice for some time.
There are practical reasons why one might be restricted to console apps---connecting remotely with no X forwarding, or perhaps being on a romantic computing date with a hopelessly ancient terminal. There are also reasons why one might need a mouse. Graphics or audio editing, games, some website layouts and many other applications call for the more analogue-ish input of a mouse.
Where does this leave software in the middle? Mail clients, web browsers, chat clients, file/directory browsers, PIM and calendar software are all types of application which could feasibly have a keyboard or mouse-based interface. Increasingly, applications are adding features which specifically require you to use the mouse. I come up against this all the time but to pick an easy example (all platforms are guilty here), OS X Finder only lets you move files by dragging with the mouse. Cut and paste was evidently too complicated for their target audience.
I'm a keyboard nut, so having to reach for my three-buttoned friend annoys me when I know that a little more work in the software would allow me to do the same thing more quickly with a quick jump from the home keys.
In my opinion graphical applications should have good support for both keyboard and mouse. I today finally caught up with Vimperator which is an addon for Firefox to make virtually all browsing functionality available directly from the keyboard using vim-like syntax. Firefox provides a good opportunity to try out different interface types with its interface being so heavily customisable using Javascript. With Vimperator, Firefox behaves exactly how I would like. I can still use a mouse when needed, and I can also do things quickly from the keyboard when my hands are there.
It took a third-party effort to get this functionality in place. Sadly I doubt that many application developers are going to put this level of thought into the keyboard interface. It is worthwhile adding that a keyboard interface is required for proper accessibility for some physically-disabled users.
I like modern software. Really. Am I so backwards to prefer pressing buttons which remain stationary on my desk?