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When using Natural or Simple weighted mean of grades aggregation*, the Moodle gradebook allows you to identify individual grade items, as well as entire categories as extra credit. By doing this, the points earned for that item or category will not be used in calculating the total points possible for its parent category, but those points will be added to the total points earned in that category.
*See the Moodle Gradebook Aggregation article for more information on aggregation types and extra credit.
Note on extra credit calculation: the extra credit item or category may not contribute to the course total as you expect until all grades have been entered. For instance, in a category with 5 items each worth 20 points (or 5 items weighted at 20%) and one extra credit item worth 5 points (or percent), the intention is that the extra credit will add up to 5% to the category total. However, if the extra credit grade is assigned a value of 5 before all five grades are entered, it will have a disproportionate effect on the total grade. If three grades had been assigned, resulting in an average of 90, the expectation is that the extra credit would bring that up to 95. However, it is not tacked on to the average, but rather used in calculating the total score, so you end up having a total of 54 for the graded items (three 20 point items at an average of 90 each - 3 * [.9 * 20] = 3 * 18 = 54), and then Moodle adds the extra 5 points to yield 59, which - when divided by the total possible points of 60 - yields a score of 98.33%. Once all values have been entered (say 5 at 90% = 5 * 18 = 90), the 5 additional points will have the desired effect ([90 + 5] / 100 = 95%).
Setting an item or category as extra credit
Whether dealing with a manual or Moodle-created grade item, or a category, the process for designating it as extra credit is the same. Starting from the Gradebook setup page (Grade item from the side menu, click on Setup tab), find the desired grade item or category, and click on the Edit link to display the drop-down menu, and select Edit settings.
On the settings page, go to the Parent category section (you may need to expand this section by clicking on the arrow to the left of Parent category), and click on the checkbox next to Extra credit, and Save changes.