Professional Gap Filling

You might also consider some of the "Plastic Welder" types of glues such as Tenax since they tend to eliminate a lot of seams in and of themselves.

I also use Squadron putty and Zap-A-Gap and have good luck with those. There is a post here: http://www.finescale.com/fsm/community/forum/topic.asp?TOPIC_ID=19822
discussing using some material called Porc-A-Filler for gap filling that seems to work very well. I plan to try it at some point, but haven't had an opportunity to do so yet.

For filling large holes you might take a look at Milliput. It is a two-part epoxy putty that does a good job of filling, but it dries hard as concrete.

You will have to try a few and see what you like.
I have the sqadron white putty and like it better than the green.
I have heard some people on this forum say that the Tamiya putty is great but I have never tried it. Still other's say that automotive spot putty is just as good as any of these and one tube will last a lifetime.
I actually use CA as a gap filler most often as it cures fast and is smoother than putty, although it can be a pain to sand sometimes as it is harder than putty.
Try a few out and see what you prefer would be my best advice.

Mike