There are two options for upgrading Eclipse Helios to Eclipse Indigo: direct upgrading and fresh install.
Option #1 - Direct upgrading
1) Click Help > Check for Updates
2) Window > Preferences > Install/Update > Available Software Sites
3) Click 'Add'
4) Enter http://download.eclipse.org/releases/indigo
5) Click 'Ok'
Option #2 - Fresh install with importing plugins from old version
Occasionally, due to incompatible changes in the update technology, you won't be able to upgrade Eclipse or certain features. So you will need to download a fresh install.
1) Download and unzip a new build from the Eclipse download Web site (http://download.eclipse.org or http://www.eclipse.org/downloads)
Next step is to import plug-ins from your previous install.
2) File > Import > Install > From Existing Installation > select your old install > select the plug-ins and there you go!
3) Click Next a couple times and wait for the updates to download to your machine.
4) Restart Eclipse
Upgrades may require administrator privileges to succeed and may fail with error messages claiming:
"Only one of the following can be installed:" otherwise. Start Eclipse with "Run as administrator...".
Complete upgrade instructions are always included in the Eclipse readme_eclipse.html file included with every build in the readme directory.