Examples of eventual counterexamples
It was once conjectured that factors of $x^n-1$ over the rationals had no coefficient exceeding 1 in absolute value. The first counterexample comes at $n=105$.
The least positive integer for which the equality $$ \left\lceil \frac{2}{2^{1/n}-1}\right\rceil = \left\lfloor \frac{2n}{\log 2} \right\rfloor $$ fails is $n=777,\!451,\!915,\!729,\!368$. See https://oeis.org/A129935.
Another example that I like is the number $f(n)$ of inequivalent differentiable structures on $\mathbb{R}^n$. We have $f(n)=1$ if $n\neq 4$, while $f(4)=c$, the cardinality of the continuum.
The essence of the phenomenon of eventual counterexamples is that a certain pattern that holds among small numbers, turns out not to be universal. In the very best examples, such as the examples provided in the other answers, which I have enjoyed very much, what we have is an easily described property $P(n)$, whose first failing instance is very large in comparison. Indeed, the quality of answer might be measured by the difference between the size of the description of the property and the size of the first failing instance of it. When an easily described property holds for a very long time and then suddenly fails at some very large number, we are surprised. Therefore, to my mind the phenomenon of eventual counterexamples is intimately wrapped up with the possibility of providing very short descriptions of enormous numbers.
Surely we are all able easily to provide short descriptions of some very large numbers, such as $2^{100}$ or $2^{2^{100!}}$. In order to go beyond exponentiation and factorials, we might make use of other easily described functions exhibiting even more enormous growth. The Ackermann function, for example, defined by a simple one-line recursion, has diagonal values 1, 3, 7, 61, $2^{2^{2^{65536}}}$, with the next value $A(5)$ mind-bogglingly huge.
All such examples, short descriptions of large numbers, can be systematically transformed into instances of eventual counterexamples. For if $d$ is a short description of an enormous number $N$, then the property $P(k)=$"$k$ does not exhibit $d$" is easily described and holds for all values $k$ below $N$, but not of $N$ itself. Thus, it does very well by the quality measure I mentioned above.
So to my mind, the real issue is: what are the largest numbers that you can describe by a very short description?
This question can be made precise by requiring the description to be expressible in a particular formal language. Once the language is rich enough, however, this problem will certainly wade into interesting foundational waters, for the question of whether a given description actually succeeds in describing a number---for example, "the length of the shortest proof of a contradiction in ZFC"---may be independent of our basic axioms, even if it is enormous.