I release a bunch of tools for free, but recently I have began to sell an application, that has private research, and people have been able to get my source code, and one person publically released my entire source. I spent a lot of time on this program, just to have someone crack it, and release my entire source.
How can I go about protecting my program? I have tried HWID, but people are still able to crack it. I know I am limited by C#, but it the most convenient to use. I just need a way to protect my programs from people trying to do this.
There's Dotfuscator (http://www.preemptive.com/products/dotfuscator/overview). But the best solution in some cases is to offer what you do as a web site (Software as a Service).
Consider this tool for example to convert VB to C#: http://converter.telerik.com/
Or this tool to format JSON: http://jsonformatter.curiousconcept.com/
This may or may not work for you. I don't know what the nature of the software you're trying to protect is.
No, your code needs to contain the information needed to decrypt itself, its an impossible problem to solve.
Your best solution is to put your intellectual property on a server in the cloud that only you have access to. Give your customers a unique login, audit their access to check for abuse, off load as much grunt work onto your customers machines, but keep your algorithms locked into the cloud.
You could have a look at the many obfuscation tools that are out there, for example the ones mentioned in https://stackoverflow.com/questions/805549/free-obfuscation-tools-for-net (note: question currently unavailable for view).
EDIT: the above linked question has been deleted and thus isn't available for viewing. As a reference here is the list of currently working links posted in the above question extracted with help of some power user:
http://gapotchenko.com/eazfuscator.net
http://orangeheap.blogspot.nl
http://confuser.codeplex.com (succeeded by https://yck1509.github.io/ConfuserEx/) http://ntoolbox.com
Well, the problem with languages like C#/Java is that they are generally much easier to de-obfuscate. The way to secure this is generally to put this stuff into a webservice, but you said you couldn't really do that. What about porting specific non-trivial functions over to a language like C, and obfuscate that. Your C# program could then use reflection to make calls to this external/unmanaged dll. It would increase the difficulty for de-obfuscating, but the problem is that if someone wants it bad enough, they can figure it out as it is client-side.
It may be that legal action is the only real solution here, but this is not a site for legal advice, and I am not qualified to give it if it were.
Additionally, this could be a business decision. Consider Making your software open-source and post a donation link. I am also not qualified to give business advice, but this is worth considering. It may actually increase your revenue, not to mention the other benefits that come with releasing open-source software.