Short of making the whole thing in pink, a quilt is more likely not to be obviously gendered. Do remember that while some parents love to colour-code their children by gender, a lot of parents don't. I've always gone for bright, multi-coloured quilts that don't read as any particular gender, and the parents have always been thrilled. My Craftsy page is at
http://www.craftsy.com/user/48661/projects, and the last three are baby quilts. With the turtle quilt, I actually used some pink for the first time ever (a few bits in the turtle shell). Normally I hate pink, and I was really self-conscious about using it at all. When it arrived, my cousin said, "Oh, thank goodness it isn't pink! Everyone else has been giving us nothing but pink!" If parents do like to do the pink for girls, blue for boys thing, they will already have absolutely plenty, and will not mind a bit of something multicoloured to add interest. And if they don't like it, they will have been overwhelmed with pink/blue whether they like it or not (apparently it is literally impossible to dress a girl from infancy onwards and avoid pink all the way through), so they will be delighted to get something different for once.
I really love working with these bright colours, it is so cheering. I've also made wholecloth quilts, or at least quilts with only one fabric per side. In the first instance, one side was a multicoloured fabric with owls and medallions and branches, and the other side was a large irregular dot fabric in two shades of blue. I tied it with embroidery thread in variegated light green, and embroidered his name on the blue side in variegated pink/yellow. In the second instance, it's going to be a proper wholecloth quilt with Welsh quilting. One side is yellow, and the other is an owl pattern with cream, yellow, orange, pink and purple. I asked the mother if she minded having a fair amount of pink in a boy's quilt, and she told me not to be daft (and indeed has lots of hand-me-downs from her family for the baby in pink).
In conclusion: bright and cheerful in a variety of colours always goes down well. And if you prefer pastels, you can easily do them in gender-neutral colours, e.g. green and yellow, or just a mix of colours. I've been told that parents often go for pastels, but babies go for brights, so I think either is absolutely fine. I've also seen a few black/white quilts, sometimes with a goth pattern if the parents are goths, sometimes just random, sometimes with something that fits the colours such as a penguin design.
In terms of fabrics, there are lots of novelty fabrics aimed at children. You don't need to use these, I mostly haven't, you can just pick pretty colours and patterns. If you do go for them, there are lots which come in a variety of colours and gender-neutral patterns, such as alphabets or zoo animals. Dinosaurs are particularly cute, I think. If the mother is a keen scientist as well as a doctor, she may enjoy some of the more science-oriented fabrics, such as animals or plants. I'm finding that I use the novelty fabrics for backing, especially in a nice soft flannel, and then ordinary quilting fabrics for the piecing. I prefer the ones aimed at children to the ones aimed at babies, I find the baby ones a bit insipid, but it's a personal thing and obviously some people adore them. I seem to have a thing for sea creatures and owls, judging by my work so far. One of these days I am going to make a dragon quilt, because they
rock.
I-Spy quilts are also popular for children, and again lend themselves well to using a variety of colours. I've seen some lovely quilts which have a big alphabet done in appliqué. There are so many things you can do with baby quilts, but they are always a joy to work on.