What exactly is the logic you would want to use to define a flapping interface, should be pretty easy to whip up a report from the event history table of any interface with more than x numer of status changes within y minutes. Or even simpler, if you don't have a particularly noisy environment just list off every interface down or up event for the last 24 hours or so.
We just had an issue this morning where a cable or SFP was beginning to freak out. "Freak out" is a technical term for those non-network types out there. The flap was detected based on syslog messages:
%DUAL-5-NBRCHANGE: EIGRP-IPv4 1: Neighbor xxx.xxx.xxx.xxx (GigabitEthernet0/0/1) is down
%DUAL-5-NBRCHANGE: EIGRP-IPv4 1: Neighbor xxx.xxx.xxx.xxx (GigabitEthernet0/0/1) is up: new adjacency
However, EIGRP is also being monitored by Orion...so that might be another method as well. Or maybe IP SLA or NetPath are options.
Just some random ideas.