What sized little pits are we talking about?
For pretty decent sized stuff, I use something like GS or Apoxie sculpt to fill in...depending on the area that needs fixing.
For smaller stuff - I use some of the Squadron model putty (reagent curing...so, some with more delicate environmental sensitivities might be offended by the presence of chemicals like toluene in materials they work with). Green or white - both work well enough, dry hard and you can sand them if you get a bit too crazy with them.
For pits, pockets, bubbles and the like that are actually pretty small - I go to the greatest of fillers in all the world...Mr. Surfacer from Gunze. The Mr. Surfacer 500 is thicker, and is wonderful with dealing with the small imperfections that can happen in resin casts as well as seams between parts (that otherwise fit together fairly well). Mr. Surfacer 1000 is a bit thinner and is mainly for dealing with stuff like scratches and the like (I use it when I grind off details...like Skulls from GW models).
As an added benefit - the Mr. Surfacer 1000 comes in a rattle can and doubles as an excellent primer (though remember - it is designed to fill imperfections...so if you have a lot of really fine details - they can disappear).