The axioms of Euclidean geometry are rarely used by mathematicians nowadays, outside of teaching purposes or historical purposes. The importance of Hilbert's axioms for Euclidean geometry (from his Grundlagen around 1899) is that he used them to present the first example of the modern concept of an axiomatic system. Hilbert improved these axioms in later editions of the book, removing redundancies. And while other writers have toyed with variations on the axioms of Euclidean geometry, with various different pedagogical goals, the object is always to have axiom systems for the same theory, that is, axiom systems that are equivalent to each other. So there's not really any way to say "these axioms are better than those ones" without some subjective criterion as a guide. Personally, I like axioms of the Euclidean plane which incorporate rigid motions, rather than axioms with two different flavors of congruence as Hilbert has (I've taught this in my classes).
On the other hand, the axiomatic method --- of which the Euclid book is the founding example (however imperfect), and the Hilbert book is the first modern example --- now pervades much of modern mathematics. Yes, there are systems of axioms throughout algebra, topology, linear algebra, set theory, analysis (including axioms of the real numbers), and so on.
Perhaps the most important axiom system nowadays is the ZFC set theory axioms. Many important definitions of mathematical structures are formulated in an axiomatic manner within set theory. For example, a vector space is usually defined as a model --- within set theory --- of the axioms of vector spaces.
Another example of an axiomatic system, one that is taught in the college math curriculum, are the axioms of the real numbers, meaning the axioms for a complete, ordered field. For this example (as for many others), one usually learns at some point how to model the axioms of the real numbers within ZFC. This is usually done in a series of steps: first one models (the axioms of) the natural numbers within ZFC; then one models the integers within the natural numbers; then one models the rational numbers within the integers; and finally one models the real numbers within the rationals, using for example the Dedekind cut method.
And one can then model the axioms of the Euclidean plane within the real numbers: a point is an ordered pair of real numbers $(x,y)$; a line is the solution set of an equation of the form $Ax+By=C$ where $A,B,C$ are real numbers and $A,B$ are not both zero; one proves that two points determine a unique line; and so on...
So with that as an example, one might say that the ZFC axioms of set theory form the "main" axiom system of mathematics (including geometry, algebra, analysis, ...).