How does temperature affect voltage references, resistors etc.?
The 0.1% means that the voltage can be 0.1% off at the rated temperature, which is usually 20°C. Since the temperature coefficient (TC) is positive and you're talking about higher temperatures you should count on +0.1%, not -0.1%, for worst case calculations. (For worst case calculations always make sure that errors add instead of cancel each other out.) 
So at 20°C your reference will be 3.003V worst case.
At 85°C the voltage may increase by 100 ppm/°C \$\times\$ (85°C - 20°C) = 6500 ppm, or 0.65%. So the voltage will be 3.003V \$\times\$ 100.65% = 3.023V.  

Yes, it also applies to resistors. Temperature coefficients range from a low 5 ppm to 250 ppm, depending on the materials used. Thick film resistors are the least temperature stable with a TC of 200 to 500 ppm. The widest variation can be found in metal film and thin film resistors, with some precision types having a TC as low as 5 ppm, while others have a TC of 200 ppm.
If you would use a resistor divider to scale down your reference voltage, choose the same type for both resistors, then you don't have to account for TCs.