Here are all the things that could be used to show that Laguna is Squalls father:

1) Laguna = Lagoon. Raine = Rain. Squall = Brief windstorm, usually with snow or rain.

All these names are connected, they are all to do with water.

2) Raine and Laguna had a child together. That child was sent to the orphanage

The children in the orphanage at that time were as we all know, Squall, Seifer, Ellone, Quistis, Zell, Irvine and Selphie.

Ellone is the adoptive sister to that newborn child, and spends a significant part of her life trying to get Laguna back to Raine and this child.

Coincidentally, who is the one person in the orphanage who Ellone is closely attached to? Squall.

Also notice how none of the other children are paid attention to at all when it comes to this plot question, and seeing as how it is a very relevant part of the game, you'd think Square didn't just decide to drop it completely.

3) In the Ragnarok, Laguna tellls Squall that "Ellone has told me everything" and "We'll talk when this is all over".

Since Ellone had just stopped her quest to get Laguna to see his newborn child, one would expect her to tell all about the child to Laguna, and it seems rather farfetched that she refused to give him the true identity.

This would also have been basically the most important thing Ellone would tell Laguna, so it seems plausible that he is going to talk to Squall on the same issue.

4) Talk to Kiros and Ward in the Ragnarok, and Ward will say "Good thing you don't look like your father" in a joking manner,
Kiros says "you look more like your mother".

Kiros and Ward know the parents, and the father well enough to make fun of him jokingly.
Who fits into this description then?

5) The tutorial tells us that Moombas recognize people by licking their blood.

In jail, a Moomba calls Squall "Laguna" many times. This means Squalls blood was so similar to Lagunas that it fooled the Moomba.

That kind of scene isn't just put in there for randomness, nor to prove that Moombas are mentally unstable.