I agree with Elarinya in that they'll have more than 3 kids, definitely. Harry shows a desire for the company of a big family early on in the books, and Hermione as an only child probably longed for a sibling on occasion - then again, more kids tends to equal more noise and fewer places to hide and read
Hogwarts, A History 
Even so, I think she'd do well as a mother to a big family of mostly boys. Since Hermione's two closest friends are boys I'd think she'd be a much better mum to boys than girls anyway. But Harry would need a little girl to spoil.
Robert Sirius nn Robbie - He'd have his dad's black hair and his mum's brown eyes, no glasses. And he'd have a few freckles across the bridge of his nose. He'd be in Gryffindor, obviously, and he'd be rather shy. Not a good trait for a son of Harry Potter, cause he has to deal with being in the spotlight quite a bit, but not as much as dear old dad. Really sweet kid who just wants to be his own person and not be "Harry Potter's son" forever.
Michael Remus nn Michael - Black hair, brown eyes, just like Robbie. He'd hafta be in Gryffindor too. Very bright and intellectual - perhaps just a bit nerdy? But not show-offy by any means. He'd be following his mother in classes like Ancient Runes and Arithmancy. Two years younger than Robbie...a good teacher and very organized.
Gabriel James nn Gabe - Brown hair, brown eyes. He'd be very athletic, a Keeper on the Gryffindor House team. With two Potter boys before him and not looking as much like his dad as them, Gabe won't suffer the limelight the way Robbie and Michael did - so he'll have to make his own claim to fame, and he'll do it through Quidditch. An aggressive Quidditch player, but he'll lack the same motivation in school - he does well enough to get by, but he's not like his brothers. He's a year younger than Michael.
Matthew Granger nn Matt - Back to the black hair and brown eyes. Matt will be a troublemaker, no doubt about it. A Gryffindor, but just barely - the hat was toying with Ravenclaw and Slytherin over Gryffindor, but he ended up there anyway. Very intelligent, both with book smarts and street smarts. Mischevious like his grandfather, and he goes a bit stupid around girls sometimes like James. Three years younger than Gabe.
Samuel Arthur nn Samuel - Samuel's got Hermione's brown hair, but he's the only Potter boy besides his dad with green eyes. Very friendly, bordering on a shameless flirt sometimes - it's the green eyes. He's incredibly charming, which he'd have to be to stand out to the girls from his brothers. He is very motivated to be an individual and be seen as a different person than Harry, Robbie, Michael, Gabe, and Matt. One year younger than Matt.
Tamsin Alexandra nn Tamsin - Tamsin has light brown hair and green eyes. She's a cute girl, outgoing, and the Gryffindor Seeker, just like dad. She's very protected by her brothers, three of which are in Hogwarts with her when she starts first year. Tamsin is very loyal and trustworthy, but she is also a somewhat assertive person. She's two years younger than Samuel.