My wife and I do limited entry hunts almost exclusively.  I have a spread sheet that organizes all our applications according to the application date and draw dates, I mark the "done" field when I have applied that year.  Here is a sample of the first few entries:
	
	
		
		
	
	
On this spreadsheet I track our points and what year I believe we should draw.
On a separate spreadsheet I track each species and state we are applying for.  I watch things like draw statistics, harvest statistics, expected season dates in future years, and the moon phase compared to those season dates.
I total up the expected draw odds for all of the hunts we apply for in a given year.  If the total draw is around 100%, statistically we should draw one tag, if its around 200% we should draw two tags...and so on.  I make adjustments accordingly.
Our back-up plan on years we likely won't draw are hunts like Montana mule deer, Wyoming antelope, Oregon archery elk, etc.