To make sure you have the application's path (and not just the current directory), use this:
http://msdn.microsoft.com/en-us/library/system.diagnostics.process.getcurrentprocess.aspx
Now you have a Process object that represents the process that is running.
Then use Process.MainModule.FileName:
http://msdn.microsoft.com/en-us/library/system.diagnostics.processmodule.filename.aspx
Finally, use Path.GetDirectoryName to get the folder containing the .exe:
http://msdn.microsoft.com/en-us/library/system.io.path.getdirectoryname.aspx
So this is what you want:
string folder = Path.GetDirectoryName(Process.GetCurrentProcess().MainModule.FileName) + @"\Archive\";
string filter = "*.zip";
string[] files = Directory.GetFiles(folder, filter);
(Notice that "\Archive\" from your question is now @"\Archive\": you need the @ so that the \ backslashes aren't interpreted as the start of an escape sequence)
Hope that helps!