Most isolation schemes use optocouplers. For analog signals you can do something like a voltage to frequency conversion and use an optocoupler (or transformer) to isolate the signal. Other possibilities are to use a serial a/d converter and optos to isolate the clock and data - this is a very popular method - see analog devices,maxim,texas linear tech for app nots for diong this. Using the one-wire device is another possibility - only two optos needed here - one for send, the other for receive. Another method is to use something like Analog Devices ADuc series, Texas MSC1210 or Cygnal devices which have 12 bit or better adcs with the cpu on chip and isolate the serial data out of them. This is the method I've used on one of my latest products - a dc/dc converter isolates the 5volts, optos isolates the RS485 comms. Simple! The optos I use here are the Sharp PC900v as they have the receiver electronics in them and are good for 1mbit data transfer.

As for your differential input problem - an op-amp can be used to sense the voltage across your 250 ohm resistor that is above 0volts and give you a single-ended output for the a/d. A Lm324 and 4 resistors does the job simply. Note- this method gives you gain and offset variations that need to be calibrated out. Have your software store the value from the a/d for 20mA and for 4mA and calculate the actual value for the input.

Burr Brown (texas instruments) have some parts that are pre-calibrated but expensive.

For some fun, try pulling apart a piece of commercial gear that does what you want - most likely you'll find the above techniques in use.