The regular expression you should use is "\n\n\n" (without the quotes). Search for this with the find panel and make sure that the regular expressions option is selected. Now do a "find all" (from the find panel), which will create multiple selections. Use your arrow keys to re-position the multiple selections so the cursors are on the second empty line (right then left worked for me). Now you should have multiple selections, each one on the second of the empty lines (exactly where you want to insert the numbers).
Now you need to insert the incremental numbers into the selections, but you'll need a plugin for that. Luckily there already is one available for you: http://www.sublimetext.com/forum/viewtopic.php?f=5&t=1604&start=0
. It might be easier to setup the plugin first (before you do the selection above).
Hope that helps.