for each blog there is an option "ping_sites" that determines which services are pinged for activity within the blog. the wpmu code allows for multiple entries within this option, expecting them to be newline \n delimited.
so, for example if you wanted to set up multiple services for a single blog youd enter sql of the following form:
update wp_2_options set option_value = 'http://rpc.pingomatic.com/\nhttp://topicexchange.com/RPC2' where option_name = 'ping_sites'
there is a function named populate_options that youll find somewhere in your install - its shifted around within different wpmu versions - that installs the default option for each new blog. if you look for the line that populates ping_sites then you can edit it so that new blogs automatically get the new ping server set.
so for example if you want to set it up so that all future blogs use a new set of ping servers, youd simply change the line that reads:
add_option('ping_sites', 'http://rpc.pingomatic.com/');
to:
add_option('ping_sites', "http://rpc.pingomatic.com/\nhttp://topicexchange.com/RPC2");
nb. the double quotes are required for the escaping of the newline character