used lookupInScope(name) to find the qualified names in comments.

pkg/docgen/lib/docgen.dart

 // Copyright (c) 2013, the Dart project authors.  Please see the AUTHORS file
 // for details. All rights reserved. Use of this source code is governed by a
 // BSD-style license that can be found in the LICENSE file.
 
 /**
  * **docgen** is a tool for creating machine readable representations of Dart 
  * code metadata, including: classes, members, comments and annotations.
  * 
  * docgen is run on a `.dart` file or a directory containing `.dart` files. 
  * 
@@ skipping 42 matching lines @@
 /**
  * Docgen constructor initializes the link resolver for markdown parsing.
  * Also initializes the command line arguments. 
  * 
  * [packageRoot] is the packages directory of the directory being analyzed. 
  * If [includeSdk] is 'true', then any SDK libraries explicitly imported will 
  * also be documented. 
  * If [parseSdk] is 'true', then all Dart SDK libraries will be documented. 
  * This option is useful when only the SDK libraries are needed. 
  * 
- * Returns true if docgen sucessfuly completes. 
+ * Returns 'true' if docgen sucessfuly completes. 

[Emily Fortuna, 2013/07/09 20:21:36]

I think you could use the backtick (`) instead, since it's a code value. so:
`true`

[janicejl, 2013/07/10 01:16:40]

Done.

  */
 Future<bool> docgen(List<String> files, {String packageRoot, 
     bool outputToYaml: true, bool includePrivate: false, bool includeSdk: false,
     bool parseSdk: false}) {    
   if (packageRoot == null && !parseSdk) {
     // TODO(janicejl): At the moment, if a single file is passed it, it is 
     // assumed that it does not have a package root unless it is passed in by 
     // the user. In future, find a better way to find the packageRoot and also 
     // fully test finding the packageRoot. 
     if (FileSystemEntity.typeSync(files.first) 
@@ skipping 191 matching lines @@
       } 
     }
   });
   commentText = commentText == null ? '' : 
       markdown.markdownToHtml(commentText.trim(), linkResolver: linkResolver)
       .replaceAll('\n', ' ');
   return commentText;
 }
 
 /**
  * Converts all [_] references in comments to <code>_</code>.

[Emily Fortuna, 2013/07/09 20:21:36]

nit: can we change this comment to say "Converts all [foo] references in
comments to <code>foo</code>."  ? I originally read this comment as converting
the underscores to code and I was confused. :-)

[janicejl, 2013/07/10 01:16:40]

Done.

  */
-// TODO(tmandel): Create proper links for [_] style markdown based
-// on scope once layout of viewer is finished.
 markdown.Node fixReference(String name, LibraryMirror currentLibrary, 
     ClassMirror currentClass, MemberMirror currentMember) {
-  return new markdown.Element.text('code', name);
+  
+  var reference;
+  var memberScope = currentMember == null ? 
+      null : currentMember.lookupInScope(name);
+  if (memberScope != null) reference = memberScope.qualifiedName;
+  else {
+    var classScope = currentClass == null ?
+        null : currentClass.lookupInScope(name);
+    if (classScope != null) reference = classScope.qualifiedName;
+    else {
+      var libraryScope = currentLibrary.lookupInScope(name);
+      reference = libraryScope != null ? libraryScope.qualifiedname : name;
+    }
+  }
+  return new markdown.Element.text('a', reference);
 }
 
 /**
  * Returns a map of [Variable] objects constructed from inputted mirrors.
  */
 Map<String, Variable> _getVariables(Map<String, VariableMirror> mirrorMap, 
     bool includePrivate) {
   var data = {};
   // TODO(janicejl): When map to map feature is created, replace the below with 
   // a filter. Issue(#9590).
@@ skipping 278 matching lines @@
     parameterMap['qualifiedname'] = qualifiedName;
     parameterMap['optional'] = isOptional.toString();
     parameterMap['named'] = isNamed.toString();
     parameterMap['default'] = hasDefaultValue.toString();
     parameterMap['type'] = type;
     parameterMap['value'] = defaultValue;
     parameterMap['annotations'] = new List.from(annotations);
     return parameterMap;
   } 
 }