Pretty sure that this has been discussed before - did you do a search?
Anyhoo, I know that ZepDT has a bunch of rarities, as does Franz, so hopefully they'll see this thread. Amongst the rarest things that I own (altho do not have in my possession at the moment) are 3 bass drum heads from MP - one from the Train of Thought tour, one from the first leg of the 20th Anniversary tour and one from the LTE reunion shows. MP sent me the first two, and signed the 20th Anniversary one (including a message) to thank me for all my work for him and DT. Later he sent me the LTE bass drum head that was used for the LA and SF shows.
Funny thing about this particular one is that it is essentially homemade. I had created the artwork for the bass drum head and sent it to MP for it to be professionally printed. He had separate kits and drum heads for the east coast, Chicago and west coast shows. The day of the LA show, somehow the bass drum head didn't arrive in time for the show. MP contacted me that morning to see if there was anything I could do. Fortunately I was working that morning and my boss was cool enough to allow me to do a digital proof print on the high end proofer we had at work (I worked in the electronic pre-press dept of a printing company) to take with me to the venue that afternoon. When I got there, I gave it to Eric Disrude who was teching for MP and he cut it out and attached it to a generic bass drum head, which is what you see if you watch the LTE Live in LA DVD!
I'm sure that I've got a few other rare/unusual items in my collection, but those are the first ones that come to mind.