Possibility 1 - Morphing Helios into Indigo
The idea here is that you will upgrade your Helios install into an Indigo one. If all plug-ins have been playing nicely in specifying their version ranges and using APIs, this should just work. Otherwise you will get presented with errors messages having unsatisfiable dependencies. Anyway, here are the steps:
Step 1: Add the http://download.eclipse.org/releases/indigo to the set of repositories (Preferences > Install Updates > Available Software Sites).
Step 2: Search for updates: Help > Check for Updates. Note that this will search for updates for all the plugins that are installed. If you want a more selective update, try Help > About > Installation Details and select the entries you are interested in updating among the elements listed in the Installed Software tab (see pictures below).
Step 3 : Once prompted with the available updates, select the desired items, click next a couple times and patiently wait for the bytes to download to your machine. Then restart and enjoy!
Possibility 2 - Start fresh and install plugins from an old install
The idea here is that you want to keep your old install intact, download a new indigo package (http://download.eclipse.org/) and just adds the existing plugins to your install. With Indigo this is now made super easy!
Step 1: Download and unzip your Indigo install: http://download.eclipse.org
Step 2: Import your plug-ins from your previous install by doing File > Import > Install > From existing install, pick your old install, select the plug-ins and there you go! You can chose to go piece meal, or chose to pick several entries, in any event dependency analysis will be performed to check the validity of the install.
Step 3: Click next a couple times and patiently wait for the bytes to download to your machine. Then restart and enjoy!