Multiple updates. See description.

Looks good! I will suggest a few things though:
1.Probe inputs looks like maybe 2.5 or 3.5mm jacks. Connect the TIP to
the analog input, and the SLEEVE or RING to GND. That way ESD has a
harder path into you Spark Core inputs.

I connected the tip and NC switch to analog in and the sleeve to gnd.

2.It might be a good idea to do a Low Pass RC filter with the inputs in
a different way so that you have a resistor always in series with the
analog input. A 1k and 1uF should be plenty fast for temperature
sensors. Then you still have your 10k pull up and thermistor pulldown on
the front end. Assuming the impedance of the ADC input is high, you
won't get much of a voltage divider effect when taking a sample. The
large 1uF cap will also help this along, effectively lowering your input
impedance.

I believe I've set this up how you suggested.  Assuming I did, this will
affect my R when calcuting temp.  Should I use low tolerance(1-2%)
resistors for the 1Ks?

3.Switch inputs could use two resistors each. I know you are using the
internal pullup resistors, but ESD again can easily get to the Spark
Core inputs from something a user is purposely touching all of the time
(i.e. the switches). Minimum 1k series, 10k pull up. Put the pull up at
the switch, not the Core, that way the switch can pull it all of the way
to ground.

Makes sense and sounds like a good best practice. I have updated.

4.I would add a diode in series right after the J6 output (input power),
just in case anyone decides to plug in a reverse polarity wall adapter.
Also a polyfuse in series with the diode.

I'm thinking you mean right after J5 input, in which case I have added
them and that totally makes sense.  Hopefully I'm not misunderstanding.

5.R18 should connect to FAN2, not FAN1 (copy/paste error wink )

Bah, fixed :)

6.I would make the fan connectors whatever the fans normally come with
to save cost... whatever you use make sure the connections are not
exposed before or after connections are made, since you have live +12V
and a switched node. Shorting GND to this by accident could cause some
issues.

I picked a connector here that seemed to be the most common among
commercially available "smoker" fans/blowers and also added standard
header pins in to more easily allow connecting anything else.  Ideally
the fan would use the barrel connector.

Also now that I'm using 1K resistors I changed the 2 330 pull downs to
1K's for less parts.