Transactional Replication - Publications with same Name on the same Domain I'm using Transactional Replication and I've currently got three 2008r2 instances Publisher/Distributor/Subscriber.

I need to put three more 2008r2 instances on the same domain in the exact same configuration.

I'll be changing the Publisher Names, but I'd like to avoid changing the Publication Names. 

I'm pretty sure this is safe to do, but in the past I've found replication to be "problematic". 

Our set-up includes little quirks such as Indexed Views materialised as Tables and I also have concerns about Orphan meta-data lurking under the bonnet.

Has anybody had any problems with duplicate Publication Names and strongly advises against them? Any shared wisdom would be much appreciated.
Yes, it is fine to have same publication names on as many different publishers as you want.  You most likely can't have dup publication names on a single publisher though, but that is not what you are asking.  Further, you can easily test this out in your test/dev environment, on two servers.  Create a single pub/dist/sub server, and on second server, create another pub/dist/sub, and on each, create a publication with same name.

About your comment "but in the past I've found replication to be "problematic" - please explain?