Interbreeding is constrained with that the offspring shares the gene pool of the parents. What are some examples of interbreeding that has occurred, where the two species were separated by 5 million years or more?
I depends a little bit about what you mean by interbreeding. In any case, my answer won't be fully satisfactory.
Horizontal gene transfer
If you are referring to any exchange of genetic materials than, you can have a look at Salzberg et al. (2001) who report 40 genes that were horizontally transferred from bacteria.
If you are thinking about some kind of more common type of inbreeding, then you might want to consider
mule who is the hybrid between a male donkey and a female horse. Donkey and horse share a common ancestor that is about 4.5 millions years old (according to Live Science). Mules are often sterile but some of them have been fertile (Rong et al. 1988; see also this article from the Denver post; thanks @iayork)
Platanus × acerifolia is a hybrid between Platanus orientalis and Platanus occidentalis. Platanus are a rather old genera with fossils of 115 millions years old found (from wiki). However, I don't know how old is the common ancestor between P. orientalis and P. occidentalis
There are plenty of other examples in wikipedia > hybrid but I failed to find good estimate of common ancestry for those who may have had a common ancestor older than 5 millions years but it probably exist given that the mule example is already 4.5 millions years old.
Here's some research about a fern hybrid converging after 60 million years:
Some yeasts in a brewery apparently after 10-20 million years: http://www.iflscience.com/plants-and-animals/distant-species-produce-hybrid-60-million-years-after-their-split/
a Goat Sheep Geep after 7 million years: https://whyevolutionistrue.wordpress.com/2014/08/03/a-new-geep-a-sheepgoat-hybrid/
for timing evolution http://www.timetree.org/