Not Really Known
I don't think there is really any definitive evidence from the books showing a particular house to be bigger or smaller. But there is also not much definitive evidence to say that the houses were not different sizes. Of course, if we assume that the houses could be different sizes, the relative sizes could change from year to year.
Throughout the series we are privy to three Sorting ceremonies.
In Philosopher's Stone we see the Sorting Hat place four students in Hufflepuff, three in Ravenclaw, eight in Gryffindor, and seven in Slytherin (technically five; the other two are only shown to be in Slytherin later).
In Goblet of Fire we see the Sorting Hat place four students in Hufflepuff, two in Ravenclaw, two in Gryffindor, and two in Slytherin.
In Order of the Phoenix we see the Sorting Hat place one student in Gryffindor and one student in Hufflepuff.
While the numbers of students sorted differs for each house, this can hardly be taken as evidence of much because we are clearly only seeing a sample of the sorted students.
In Order of the Phoenix there are a disproportionate amount of Gryffindors in the D.A. (15/28, as you can see in my answer here). However, this likely does not indicate that Gryffindor was a bigger house; rather, Gryffindor probably had more D.A. members than the other houses because most of Harry's friends/acquaintances were in Gryffindor.
In the final Quidditch match in Prisoner of Azkaban it seems that Slytherin makes up a quarter of the school:
Three-quarters of the crowd was wearing scarlet rosettes, waving scarlet flags with the Gryffindor lion upon them, or brandishing banners with slogans like “GO GRYFFINDOR!” and “LIONS FOR THE CUP!” Behind the Slytherin goal posts, however, two hundred people were wearing green; the silver serpent of Slytherin glittered on their flags, and Professor Snape sat in the very front row, wearing green like everyone else, and a very grim smile.
This would be consistent with equally sized houses, but it doesn't prove that the houses are equally sized.
We can surmise that, at least in Harry's year, Hufflepuff and Slytherin were equal in size. In Philosopher's Stone Harry has both a Flying class and a Potions class with Slytherin in which 20 slots are mentioned:
The Slytherins were already there, and so were twenty broomsticks lying in neat lines on the ground.
Twenty cauldrons stood steaming between the wooden desks, on which stood brass scales and jars of ingredients.
And he has a Herbology class with Hufflepuff in Chamber of Secrets which also has 20 slots:
About twenty pairs of different-colored ear-muffs were lying on the bench.
Unless there were extra materials, this would indicate that Hufflepuff and Slytherin are equally sized, because if X+Y=Z and X+W=Z then Y=W. Since we also know from above that there were at least seven Slytherins in Harry's year, the Gryffindors couldn't have been much more than half, so it is likely that all three of those houses are roughly equally sized. On that note, I have elsewhere tenuously suggested that Ravenclaw may have been significantly larger than the other three houses in Harry's year, in order to account for the otherwise small number of total students and the fact that Ravenclaw is the one house that we never see Harry sharing a class with. However, that is still just a theory. Now for some vague circumstantial evidence:
We do know that each house has a long table in the Great Hall, and there doesn't seem to be any indication that the tables are not the same size. And the tables are at times described in general terms that indicate that they are pretty full. For example, in Chamber of Secrets when Harry and Ron look through the window at the start-of-term feast:
Innumerable candles were hovering in midair over four long, crowded tables, making the golden plates and goblets sparkle.
Or in Prisoner of Azkaban at the start-of-term feast:
It was a sea of pointed black hats; each of the long House tables was lined with students, their faces glimmering by the light of thousands of
candles, which were floating over the tables in midair.
Or in Chamber of Secrets when Percy asks Ginny for his seat, possibly implying that there weren't too many open seats:
"If you've finished eating, I'll take that seat, Ginny. I'm starving, I've only just come off patrol duty."
So it doesn't seem like some houses are only filling up half their allotted space, which would again be consistent with pretty equally sized houses.
On the other hand, it is probably unlikely for the house qualities to be evenly split four ways every single year, so from a statistical perspective you might expect that there should be a "biggest house".