Depending on the size of the organizations/networks, I'd say BGP would be your best/easiest bet using private AS's (65000+).
That way you can control redistribution and not have to worry about overlapping addresses being an issue. This also gives you finer control over diverse paths in terms of what should route which way...
That's how I'd do it.
You could also run a seperate OSPF process on the interconnecting routers and control redistribution that way...
Or, depending on the layout of your network (if required) you can look at using a virtual-link to connect the two through a third (interconnect) area (if you're not worried about overlapping addresses)... though keep in mind virtual links aren't recommended for production networks. http://www.cisco.com/en/US/partner/tech/tk365/technologies_white_paper09186a0080094e9e.shtml#t17
Just recently merged networks with a huge company that acquired ours.
Since we were both running OSPF and had overlapping subnets, we created an EIGRP environment in between. We created redistribution route-maps and NATed towards both OSPF backbones. It has been working.
Hope this helps.