GGM,
There were no problems with the Seniority Lists at East/Go or Ryan/Buzz, they don't have any!
The norm in the States seems to be that the pilots in the company taken over go to the bottom of the others list. This meant a lot of very experienced guys from the likes of TWA getting the elbow post 9/11.
In Aus, the Qantas/Australian Airlines tie-up saw a type of merged list known as a "Y" seniority list. Basically, you kept your position in what was considered your side of the business(long haul or domestic), were at the bottom of the "other" sides list, with all subsequant joiners on one list behind the incumbents.
Not sure how various mergers have worked in the UK (E.G. BOAC/BEA?). Anyone care to enlighten us?