Using Notepad++ find and replace with regular expression

I think this would do it for you, I'm mac based so I don't have notepad++ but this works in dreamweaver. Presuming each expression is one line based.

Find:

\(.*?"(.*?)","(.*?)".*

Replace:

<a href="$2">$1</a><br/>

File:

(7,0,"Icons Used in This Book","final/pref04.html");
(8,0,"Command Syntax Conventions","final/pref05.html");
(9,0,"Introduction","final/pref06.html");
(10,0,"Part I: Introduction and Overview of Service","final/part01.html");
(11,10,"Chapter 1. Overview","final/ch01.html");
(12,11,"Technology Motivation","final/ch01lev1sec1.html");

After Replace All:

<a href="final/pref04.html">Icons Used in This Book</a><br/>
<a href="final/pref05.html">Command Syntax Conventions</a><br/>
<a href="final/pref06.html">Introduction</a><br/>
<a href="final/part01.html">Part I: Introduction and Overview of Service</a><br/>
<a href="final/ch01.html">Chapter 1. Overview</a><br/>
<a href="final/ch01lev1sec1.html">Technology Motivation</a><br/>

If it isn't one line based change .* to .*?\n. That should make it stop after each newline. For readability you also may want to add a newline to the replace.

Should probably explain the regex as well in case you want to modify it...

The first \ is escaping the ( so the regex knows to look for the literal character and the not special regex grouping. The *? says find every character until the first "; (. is any single character, * is zero or more occurrences of the preceding character, and ? tells it to stop at the first occurrence of the next character, "). The last .* says keep going with the search. The ( and ) around the .*? group the found value into the $1 and $2. The number correlates to the order in which it is in the regex.