Are there any services that can reasonably guess what IP address a transaction originated from? Are there any services/agencies running a large number of nodes so that they can guess the IP address of a transaction's origin? 

I guess they would need to run tens of thousands of nodes. However it'll be useful in tracing stolen coins. Surely there must be some. 

I have seen talks and papers claiming to do so but not found any such service.
I see this as a non-issue. By using Tor the IP address of the originator is sufficiently obfuscated.

See my two other posts for some discussion and related resources:

How can I setup Bitcoin to be anonymous with Tor?

What are main advantages of Bitcoin over Monero?