In addition I would like to add "Vectorbase", the curator "Dan" is a good guy (I forget his surname right now) and it's a good team. However, please read my rather somber assessment of arthropod genomics first.
We appear to be talking about lower metazoans, e.g. not protists, or yeasts (the latter I suspect are really good for your question). I don't know anything about worms.
Its important to understand that arthropods are several (soccer) divisions lower than mammals in terms of the question you are asking, except for two model organisms.
Flybase, Drosophila melanogaster is the most important species for your purposes. The second most important species within the Class Insecta will be Anopheles gambiae (malaria mosquito).
Personally I would stick to the main players because overall whilst there are a lot of insect genomes (because there are a lot of insects), their genomes remain rough because of the difficulties in assembly and requirement to physical mapping their genomes in comparison to their genome size. Also except for D. melenogaster the (incredible) tardiness in producing a draft genome. For example the idea of PacBio is in its infancy for many entomologists: and this would help them a lot in assembling their genomes correctly. I agree things have picked a lot recently, but I remain a skeptic.
Within the arthropods I would be very surprised if the crustacea, myriapods or Chelicerata (e.g. spiders) were in better condition than hexapods.
If you are interested in protists certainly Plasmodium falciparum (African malaria) has the sort of information you seek (Plasmodb).
I don't want to discourage you, insects are great, but you need to be selective if you are from a human/mammalian genetics background.