GMST Contamination is the inclusion of certain default values for GMST records in a mod. This inclusion happens whenever a modder uses TESCS to create or modify an esp file that does not have either Tribunal or Bloodmoon as a master. Since some of these default settings are incorrect, the contaminated mod can break certain aspects of gameplay, notably those some spells summons and some aspects of werewolf behavior.
GMST contamination may be removed by manual cleaning or by using any of several cleaning tools (e.g., TESTool). It can also be prevented from happening in the first place through use of GMST Vaccine (archive).
GMSTs are records in mod files that control game settings. They affect many aspect of gameplay, including disposition responses, text strings, summoning spells, etc. The original Morrowind has several hundred of these, while Tribunal and Bloodmoon each added smaller numbers (primarily concerned with companion interactions, werewolf behavior and additional summons).
When editing a mod, TESCS will automatically add default values for these GMSTs into the mod if they have not already been defined by one of the loaded mods. This automatic inclusion is the source of GMST contamination.
Since GMST contamination is well known, and since tools for avoiding and repairing it are readily available, it is expected that any currently released mod should be free from such contamination. On the other hand, it is also the reality that contaminated mods are still out in the community, and so advanced players are also expected to be familiar with at least one of the GMST removal tools.
Note that that not all GMSTs are evil! Many mods intentionally change GMSTs in order to change behavior of the game. So the mere presence of GMSTs in a mod is not a cause for alarm. However the presence of 72 GMSTs in the mod (typically starting with sTeleportDisabled and sLevitateDisabled) is certain sign of contamination. In general, using TESTool to remove GMSTs is always safe.
GMST contamination can be avoided by including either Tribunal or Bloodmoon in the load list when editing a mod. Since both expansions contain the full suite of GMSTs, TESCS will not add them. However, this will make the mod dependent on the expansion which is oftentimes undesirable. (Note: Such an unwanted dependency may be removed from the finished mod with a tool like Wrye Mash.)
Contamination can also be avoided by including the GMST Vaccine mod whenever you edit your mod. Since GMST Vaccine includes the Tribunal and Bloodmoon GMSTs, TESCS won't add those GMSTs to your mod. And because GMST is not an esm, your mod won't become dependent on it. Also, since GMST Vaccine contains not the default, but rather the correct values for the GMSTs, you will have the correct info available to you as you mod (in case you want to make use of or modify one of those GMSTs). Also GMST Vaccine has an early mod date, and so is easy to find the mod list of TESCS (it's usually the first esp after the esms).
You can manually clean GMSTs from a mod by using the details view of the load dialog of TESCS. Simply select the GMSTs in the detail view and delete them. However, a simpler (and safer) approach (especially for non-modders) is to use one of the GMST Contamination removal tools -- e.g., TESTool.
Note: TESTool's GMST cleaning is safe because it only removes GMSTs that have the default value. If a mod intentionally overrides the GMST, then it will have a non-default value, and TESTool won't remove it. However, note that TESTool has many functions other than GMST cleaning, and not all of those are as safe as its GMST cleaning function.
Another approach is to override GMST contamination by including GMST Fix at the end of your mod list. The approach of this mod is to simply redefine the GMSTs to their correct values. And since it loads last, it will override any GMST contamination that has occurred. (GMST Fix is included with in Wrye's GMST Vaccine mod.)
However, overriding is not always desirable since it also overrides intentional changes to the Tribunal/Bloodmoon GMSTs. As a result, it can break the behavior of mods that modify werewolf behavior and/or summoning spells. In short, it's a lot simpler than cleaning all of your mods, but on the other hand, might break a few of them.