I would consider using a water soluble dye first (just wipe on). Then shellac. I have had good luck with this method when restoring doors.

Here is a link that might be useful: Lee Valley Dyes

Look at faux graining techniques to disguise the wood filler. Basically you use a fine artists brush to extend the flanking grain lines across the filled area. If the color match of your filler is reasonable this does wonders to hide the repair.

I use a process similar to what rwiegand describes. After staining the wood with a stain or dye but before finishing with shellac use some artist paints to color the wood filler and paint specs to match the wood colors. I picked up some oil paints at the local art supply shop and a little pallet and mix the colors to match as I go. I have zero artistic skills but was able to color match and cover the spots that were visible. Once the touch up dries, finish up with shellac and viola!

Thanks everyone, this gives me lots of good ideas! I have some of the Lee Valley dyes, so it's time to experiment. The doors are pine, maybe fir, so I'll have to find something light-coloured.