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

pkg/docgen/lib/docgen.dart

Index: pkg/docgen/lib/docgen.dart
diff --git a/pkg/docgen/lib/docgen.dart b/pkg/docgen/lib/docgen.dart
index 76cb0bb6299763dfc982b338b18e3a770246973f..7885343311c5b7432ea7aacbbcdf268169f0dc24 100644
--- a/pkg/docgen/lib/docgen.dart
+++ b/pkg/docgen/lib/docgen.dart
@@ -60,7 +60,7 @@ markdown.Resolver linkResolver;
  * 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,
@@ -274,11 +274,23 @@ String _getComment(DeclarationMirror mirror) {
 /**
  * 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);
 }
 
 /**