My personal recommendation would be to use Super/Krazy Glue for any small "cracks" in the rubber. I have successfully used it on rubber and it is quite effective!
for the slightly larger holes than cannot be filled using a liquid glue, I would recommend the following:
Apply a Gore-Tex or similar patch along with some "Shoe-Goo" or similar product. **After you have applied your patch and goo you can always add a layer of super glue over the top for added protection.
I would not recommend using a bicycle tube patch kit as they are very weak and my personal experience with them has only been awful. I actually now use Krazy Glue on any pinch flats, it has saved me a lot of money and not to mention has worked flawlessly!
If Krazy Glue can hold 110PSI of air inside a thin rubber tube, I am almost positive it will keep the water out of your boots!
**Do not get the Krazy Glue on the Gore-Tex patch, it will destroy it! Krazy glue can be used on rubber but it will destroy any fluoropolymer such as Gore-Tex!