Its a tough conversation because as you know there are not actual "pony valuers"...but at the same time auction prices are not necessarily right as sometimes we pay too little and sometimes we pay too much. As much as you are right about the random 99pm Rapunzel being undervalued if that was a finished price, likewise if we pay £80 for a Baby Gusty [for whatever reason - bidder war or just that we "must have her"] thats not a fair price either.
When I spoke to an insurer they asked for a breakdown of everything - a total for each "item" [1 item would be Red Roses with her ribbon, barrette and comb]. Personally I have gone with "valuations" on what the item sells at - i.e. an ebay search and a search here will give you an average for her price [although this is prone to change maybe its just that you will have to adjust value over the years - as with many collectable items what they are "worth" in 2003 may not be the same as in 2013]. The key is surely to simply insure for the total value of the collection and get documentation on the number of ponies and items within that collection in order to "justify" that total valuation. Individual insurance companies will no doubt look on this differently.
Its a lot of work but I guess its best to work your way back through the 1000odd ponies you have - take a picture, number the picture, add the "value" against the number on a spreadsheet.