Bro's uids are currently 64 bits, which makes them collide with a 50% chance after 5.1 x 10^9^ different uids (see http://en.wikipedia.org/wiki/Birthday_problem#Probability_table).
I'm currently generating uuids of 128 bit to replace the native uids in bro, as I'm using them as keys in a database, but this requires rewriting of the bro-logs. I suspect that more people could benefit from an option to extend the uids to 128 bit.
I've made a quick and dirty patch to change most of the uids to 128 bit (file_analysis uids are missing). The patch is ugly, and is only to show some of the functionality I would like: http://pastebin.com/GkaGejNc