One of the questions that comes up often - usually after somebody comes across one of the C# decompilers, such as RemoteSoft's Salamander or Lutz Roeder's Reflector - is “how do I keep somebody from reverse-engineering my assemblies and stealing my code?”.
While reverse engineering of code has been around for a long time, the combination of IL and rich metadata in systems such as Java and .NET make it easier. Reverse engineering optimized x86 code is harder, but it's still quite feasible, as many companies that used copy protection back in the 80s found out.
One way to think about securing your code is to consider how you secure your house or business. There are some possessions that are not protected, some that are secured with simple locks, some are put in safes, and some warrant a vault with a 24-hour guard. I think it depends upon how valuable a specific piece of software is, and that obviously is something you'll have to decide for yourself.
As for protection, there are a number of different schemes that customers have told me about.
I should also point out that there are some products that claim to use encryption-based approaches to prevent reverse-engineering, but I don't have any credentials to evaluate such schemes, so I won't venture an opinion.
If you know of any other schemes, please add them in the comments