Assuming I have a healthy wireless/wired network, in general what method has the least latency?
MX-5000 -> IP
MX-5000 -> RF -> MRX-1 -> IP
MX-5000 -> RF -> MRX-1 -> IR

MX-5000 -> RF -> MRX-1 -> IP
Doesn't work this way...

A lot will also depend on the device, as not all devices have IP...

I personally would go RF>MRX-1(2)>IR unless there's a compelling reason for IP (2-way?).

I use a mix of the 1st and 3rd methods. As JoeFlabitz said, the 2nd method is not possible. The 2 methods I use are both very quick on my MX-5000 with no detectable latency. However there is a huge downside with using IP on the MX-5000, it can take as long as 30 seconds to wake up if it has gone to sleep. Increasing the sleep delay time will cause the battery to drain much faster. The bottom line is that the MX-5000 is a power hog and you have to find a compromise between availability and battery life. This is my biggest complaint with the MX-5000.