There is insufficient information to completely answer the question.
I assume you are concerned about EMI from external sources affecting your thermometer -- not the other way around.
Questions to ask:
- What kind if EMI is your system going to be exposed to?
- What exactly are you worried about? Damage to the uC, damage to the
sensor, both?
- Corrupted Data?
- Consequences of actual EMI. E.g. danger to equipment or humans, down time, cost.
Taking these in turn:
Likely sources of EMI are from switching transient of high power local loads, especially inductive ones (motors). Nearby high power RF transmitters may also cause problems but cell phone tower are usually not an issue. Static electricity discharge can damage electronic devices too, but that is independent of the cable length.
Damage to the uC and sensor is unlikely if your sensor is connected to the uC by 3 wires in the same cable. Any noise will be mostly "common mode" (all wires are equally affected). You can put a few turn of the entire cable through a ferrite ring core if you are really paranoid.
A suitable RC filter on the uC pin(s) connected to the DQ signal may be appropriate. The details depend on your circuit. E.g. do you use 1 pin with direction control or separate read/write pins, etc?
If your concern is that you might get incorrect readings, then the CRC in the data stream will allow you to detect that and discard occasional bad readings.
Consequences of EMI: EMI protection can be expensive. If there are no dangerous consequences then replacing your thermometer may be the most economical option.
Summary: Your circuit may be fine as is, nothing further required.
The Maxim application note on 1-wire networks may help. See Appendices. The circuit in Appendix B looks appropriate for your application. Guidelines for Reliable Long Line 1-Wire® Networks
1) Understand what the noise source is.
2) Understand what the antenna is.
3) Understand how the noise gets onto the antenna.
4) Do your fix (which involves reducing the noise source and/or destroying the antenna and/or reducing the coupling to the antenna)
In most cases I have seen, you can make a single board silent enough to pass EMI without having to resort to shielding cans. The trick is a quiet power distribution network (PDN) on the board, which gives you very low impedance over a wide frequency range. Values in the range of 1-100mOhm are common. Use PDNTOOL.COM to check.
Whenever you have multiple boards interconnected, in most cases I have seen you do need a Faraday cage around the whole thing. The trick here is to "short" all cable shields to the Faraday cage right where they exit. In this context, "short" is for all frequencies of interest (where you have problems passing EMI). In your case with two isolated sections, you will have to use AC coupling for everything exiting one section. Make sure that AC short is good at the frequencies you are interested in. Even a small 0603 cap is no good above 1-200MHz.
Filtering of input/outputs for frequencies above the useful frequency range is also required in most cases I have seen. This can usually be achieved using caps and resistors, but depends on your signal types.
As for your idea about using ferrite beads, make sure you understand how they work (impedance versus frequency and tolerances). I have not seen any cases where they were required.
If you have a case, where you can't get the single board silent enough, you can use a shielding can. In this case you could either make the can shield one or both sections of the board. Either way, you would treat the "can area" like a Faraday cage - just as explained above.
Finally, let me stress one thing: understand. If you skip easy on this, make sure you have plenty of time :-/
Best Answer
IC's (as a rule of thumb) don't like floating pins but connectors are just totally passive in nature and don't care.
A floating input pin of an IC can be problematic - not only can it cause logic errors (if part of a logic device) but it can cause analogue errors. This is generally the case when the pin should have been connected to a defined voltage point such as 0V.
However, some chips will have information in their data sheets that tell you not to do anything with certain pins and you have to respect the IC supplier's instructions. I've seen this on a few voltage references.
Connectors don't care but you might decide that to reduce the possibility of EMI susceptibility that unused pins are grounded to the case thus reducing the "aperture" created by a bunch of unconnected pins.