We have a multi tier app with an asp.net and winform interface that also supports remoting. I've had no problems with using any obfuscator with the exception of the encrypting type which generates a loader which can be problematic in all sorts of unexpected ways and just not worth it in my opinion. Actually my advice would be more along the lines of "Avoid encrypting loader type obfuscators like the plague". :)
In my experience any obfuscator will work fine with any aspect of .net including asp.net and remoting, you just have to become intimate with the settings and learn how far you can push it in which areas of your code. And take the time to attempt reverse engineering on what you get and see how it works with the various settings.
We used several over the years in our commercial apps and settled on Spices obfuscator from 9rays.net because the price is right, it does the job and they have good support though we really haven't needed the support in years anymore but to be honest I don't think it really matters which obfuscator you use, the issues and learning curve are all the same if you want to have it work properly with remoting and asp.net.
As others have mentioned all you're really doing is the equivalent of a padlock, keeping otherwise honest people out and or making it harder to simply recompile an app.
Licensing is usually the key area for most people and you should definitely be using some kind of digitally signed certificate system for licensing anyway. Your biggest loss will come from casual sharing of licenses if you don't have a smart system in place, the people that break the licensing system were never going to buy in the first place.
It's really easy to take this too far and have a negative impact on your customers and your business, do what is simple and reasonable and then don't worry about it.
