Instead of wood filler. You could plane thin tapered strips and glue them in any gaps that seem excessive. That would be much less noticable. 

I had a lot of issues with this when I started on my hull, especially when I did tapers and pushed them in too hard...which would create a gap in the next piece. I also had some darker wood that splintered after I put it in and so ended up with gaps.

I made the mistake of putting some commercial wood filler in those gaps, and then had real problems with the wood filler being too light once I started fibreglasssing. In any event, if you do use commercial wood filler, make sure it's water soluble (sp?) so that it won't interfere with fiberglass adhesion.

First, try to fill larger gaps with small strips of wood the same color, as mentioned by Dave. 

In his book, Nick also suggests taking the wood dust from sanding and mixing in a little wood flour with glue to fill the gaps. If you don't add wood flour, the wood dust/glue patch will be too dark. You can experiment with a test patch and after it dries, test for a color match by wetting it. I've found that the fiberglass really darkens the wood dramatically, and if the patch is a little dark, it looks fine. 

Good luck.

I want to correct something. I went and checked and on page 135 of Nick's book, "Building Strip Planked Boats," he writes, "If you saved sanding dust when sanding the boat, you can use the dust mixed with epoxy to make filler. Even though this dust may have come from the same wood as the strips, it will appear darker than the surrounding wood. Add a little bit of lighter color material such as colloidal silica to match the color."

So, what I suggest is that you fix large gaps with wood as Dave mentions. For small gaps that open up when sanding, save your sanding dust and wait until you're in the fiberglassing stage. Us Nick's technique with dust, resin and colloidal silica to patch the small gaps. I think you can get colloidal silica from the West system line of fiberglass resin.

I read Nick's book before I started building and then referred to it as I went along, but didn't see this patch technique until I had already screwed up my gaps with commercial filler. I wish I'd used Nick's technique. 

If there is an opening where strips have separated, Nick has a video showing how to use two small blocks hot glued to the strips and then clamping them to each other to close the gap using cryanolate (sp?) and accelerator to glue the gap closed.  He then planes and sands the strips off, to avoid having to pry them off which would pull bits of the strips away.