Is there any way to increase the mysql reserved pool for super users beyond 1?
Is there some sort of sane upper limit any one user should never exceed?  Maybe your busiest application  has at most 20 open connections during peak normal operation.  Let's assume you have 20 non root users.

set max_user_connections = 30 (to give a bit of a safe buffer)

set max_connections = max_user_connections * # users + extra buffer, 
   or 30 * 20 + 50 = 650 max connections.  


This way your global max connections is safe from every getting reached and there should always be room for you to get in even if one particularly application or user is getting maxed out.