The sets that we consider are actually hereditary sets meaning that all of their members are themselves hereditary sets. What this informally means is that a hereditary set is a set of sets of sets of sets, etc.
For example, the empty set ($\emptyset$) is a hereditary set because it has no members so all of its members are vacuously hereditary sets. Then $\{\emptyset\}$ is a hereditary set because its only member is a hereditary set. Then $\{\emptyset, \{\emptyset\}\}$ is a hereditary set because both of its members are hereditary sets, and we can continue this process of tacking on the previous hereditary set as a member ad infinitum to get an infinite collection of hereditary sets. This process describes how the Natural numbers are constructed:
$0 = \emptyset$
$1 = \{\emptyset\} = \{0\}$
$2 = \{\emptyset, \{\emptyset\}\} = \{0, 1\}$
$3 = \{\emptyset, \{\emptyset\}, \{\emptyset, \{\emptyset\}\}\} = \{0, 1, 2\}$
$\vdots$
$n + 1 = \{0, 1, 2, \ldots, n\}$
By the axiom of infinity, there exists an inductive set (set that contains $0$ and the successor of any of its members) so the class of Natural numbers is actually a hereditary set. The integers can then be constructed from the Natural numbers by considering equivalence classes of ordered pairs of Natural numbers where $(a, b)$ is equivalent to $(c, d)$ exactly when $a + d = b + c$ so $(a, b)$ will correspond to the integer $a - b$. Ordered pairs of hereditary sets are also hereditary sets because $(a, b)$ can be formalized as $\{\{a\}, \{a, b\}\}$. Consequently, the class of integers will also be a hereditary set.
The set of Rational numbers can then be defined as equivalence classes of ordered pairs of integers so it too will be a hereditary set. The Real numbers, which can be constructed by considering select subsets of Rational numbers (or elements from the powerset of the Rational numbers), is also a hereditary set. Once we formalize the Real numbers as a hereditary set, we can show that a function from the Reals into the Reals, which is a collection of ordered pairs of Reals, is a hereditary set. Then we can show that the collection of all functions from the Reals into the Reals is a hereditary set. In short, all of the natural objects would be "small classes" because they can be formed from the axioms of set theory (ZFC).
The point here is that what determines whether a class is "small" or not is not whether it contains elements that look like sets such as $\{1, 2, 3\}$ or $\{a, b, c\}$ because we mostly restrict ourselves to hereditary sets anyway. Instead, we have as a minimal requirement for smallness that the objects can either be provably constructible from the axioms of ZFC or the assumption of their existence as sets does not lead to a contradiction in ZFC. I include the first possibility here because we cannot prove (within ZFC) that the axioms of ZFC won't themselves lead to a contradiction.
As an example of what we would consider a large class is the class of all small classes or the class of all sets. This is because such a class cannot be constructed from the axioms of ZFC, and it provably leads to a contradiction from ZFC (see Russell's Paradox from Brad's post). In a nutshell, if we called the class of all sets $X$ and $X$ were a set, then $A = \{x \in X| x \notin X\}$ would have to be a set by the comprehension axiom. But then $X \in X$ since $X$ is the class of all sets so $X \in A$ if and only if $X \notin A$, an immediate contradiction. Other examples of "large classes" include the class of ordinals or as Ricky mentioned any object that does not fall into the $V$ hierarchy.
One more thing I should mention here is that you should always be aware of the context when considering whether an object is a large class (also known as proper class) or not. Specifically, most of the natural objects that you consider will be small classes with respect to the set-theoretic universe. However, sometimes classes are considered with respect to individual models. A Grothendieck Universe for example, is a proper class if there are no inaccessible cardinals and we cannot prove that such a large cardinal is even possible from the ZFC axioms of set theory. As another example, we sometimes do not allow ourselves use of all of the ZFC axioms, and the set of all even numbers for example would be a large class if we explicitly assumed that all sets were finite.