I love logcheck, but I consistently find I need to use a number of custom rules to keep the noise down. Managing those rules in a central source control repository makes sense if you need to maintain multiple servers, but logcheck makes this difficult by requiring your rule files to be placed in the same directories as the builtin default rules.
To work around this issue I have written a small Python script that will symlink the rule files from your repository into the appropriate logcheck directories. The git repository includes the custom rules I am personally currently using, but you can of course easily replace those with your own.