Amazon enforces limits on how many calls you can make per hour and per second.
You can increase the former by following the sanctioned route (increase commission revenue) or by privately petitioning Amazon with a valid reason. When whitelisted, your limit will go up to 25,000 calls per hour, which is more than good enough for the vast majority of projects I can think of.
The latter limit is murkier and enforced depending on the type of query you make. My interpretation is that it is meant to keep serial crawlers who do batch item lookups in check. If you are simply doing keyword searches etc., I would not worry so much about it. Otherwise, the solution is to distribute your calls across multiple IPs.
One other point to keep in mind if you are querying multiple locales is to use separate accounts per locale. Some locales are grouped and will count to the same call quota. European Amazons, for instance, form such a pool.