I've been trying to stay away from using the communitrons to send data back to Kerbin due to loss of content/data, and was wondering how Surface Samples are stored. For example, if I wanted to take multiple samples from the Mun in one mission, could I use a Hitchhiker Storage container to store 4 different biome samples, or could I only store one sample per command/storage module?
First of all, transmitting results doesn't make you lose anything. Transmitting and then repeating the experiment and returning always makes you end up with more science points in the end than just performing and returning the experiment once.
In the current version (23.5) each command pod can store exactly one surface sample per biome. However, the number of biomes isn't limited, so you can pick up samples from multiple biomes during one mission and store them all in one pod. To gain more science out of each "Surface sample from [Object]'s [Biome]" activity, you need multiple samples. When your lander has multiple command pods (the hitchhiker pod counts as a pod for this purpose), it can store a sample of each biome in each of them, so you can retrieve more science in one mission. However, the returns are diminishing.
Each returned sample gives you 75% of the remaining science points. A second sample gives you 75% of the remaining 25%, so two samples give you a total of 93.75% and three samples 98.4%. You can never reach 100%, no matter how many samples you return. That means a second pod on one lander might be justified, but more pods are usually a waste of payload mass.
However, when you take a sample, transmit it, take another sample, and return it, you still obtain 80% of the maximum science points which is almost as much. Considering that an antenna and a few batteries and solar panels have a lot less mass than a second pod and that you likely carry that stuff anyway to transmit crew reports (from which you can store only a single one per pod), this might be the more economical option.
This answer is outdated since several versions! Please refer to my new answer which was written as of version 23.5
Every command pod can only store one surface sample. To return multiple samples you need to put multiple command pods on your lander and put a sample into each of them.
But note that using antennas to send back data does not mean that you earn less science points in total, because the reduction of scientific value is also affected by the transmisssion penalty. The total amount of science points you can squeeze out of a certain science activity at a certain location always approaches a fixed value, no matter what method you use to extract it.
That means that as soon as you have solar panels and thus an unlimited energy supply there is little reason to return research results instead of just repeatedly transmitting them and repeating the experiment.
You can store only 1 sample per pod per biome. So if you're on Mun's highlands you can store a sample from there and jet down to the lowlands, pick up another sample (and EVA report) and store it in the same pod.
I've had 6 reports (3 EVA reports and 3 samples) in the one pod but I'm unsure if there is an upper limit.
I'm uncertain as to whether you can store two of the same biome samples in different pods if they are connected.
Even though it's not technically a pod, the Hitch-hiker Storage Container can store samples in the same way.