Fade Effect on Link Hover?

Nowadays people are just using CSS3 transitions because it's a lot easier than messing with JS, browser support is reasonably good and it's merely cosmetic so it doesn't matter if it doesn't work.

Something like this gets the job done:

a {
  color:blue;
  /* First we need to help some browsers along for this to work.
     Just because a vendor prefix is there, doesn't mean it will
     work in a browser made by that vendor either, it's just for
     future-proofing purposes I guess. */
  -o-transition:.5s;
  -ms-transition:.5s;
  -moz-transition:.5s;
  -webkit-transition:.5s;
  /* ...and now for the proper property */
  transition:.5s;
}
a:hover { color:red; }

You can also transition specific CSS properties with different timings and easing functions by separating each declaration with a comma, like so:

a {
  color:blue; background:white;
  -o-transition:color .2s ease-out, background 1s ease-in;
  -ms-transition:color .2s ease-out, background 1s ease-in;
  -moz-transition:color .2s ease-out, background 1s ease-in;
  -webkit-transition:color .2s ease-out, background 1s ease-in;
  /* ...and now override with proper CSS property */
  transition:color .2s ease-out, background 1s ease-in;
}
a:hover { color:red; background:yellow; }

Demo here

I know in the question you state "I assume JavaScript is used to create this effect" but CSS can be used too, an example is below.

CSS

.fancy-link {
   color: #333333;
   text-decoration: none;
   transition: color 0.3s linear;
   -webkit-transition: color 0.3s linear;
   -moz-transition: color 0.3s linear;
}

.fancy-link:hover {
   color: #F44336;
}

HTML

<a class="fancy-link" href="#">My Link</a>

And here is a JSFIDDLE for the above code!

Marcel in one of the answers points out you can "transition multiple CSS properties" you can also use "all" to effect the element with all your :hover styles like below.

CSS

.fancy-link {
   color: #333333;
   text-decoration: none;
   transition: all 0.3s linear;
   -webkit-transition: all 0.3s linear;
   -moz-transition: all 0.3s linear;
}

.fancy-link:hover {
   color: #F44336;
   padding-left: 10px;
}

HTML

<a class="fancy-link" href="#">My Link</a>

And here is a JSFIDDLE for the "all" example!

You can do this with JQueryUI:

$('a').mouseenter(function(){
  $(this).animate({
    color: '#ff0000'
  }, 1000);
}).mouseout(function(){
  $(this).animate({
    color: '#000000'
  }, 1000);
});

http://jsfiddle.net/dWCbk/

Try this in your css:

.a {
    transition: color 0.3s ease-in-out;
}
.a {
    color:turquoise;
}
.a:hover {
    color: #454545;
}

Fade Effect on Link Hover?

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