Is this guy mentally capable of managing his own affairs? Do you suspect that the "bad guys" are intimidating him in some way, preventing him from involving law enforcement? Those are the only two circumstances where I would feel at all comfortable getting involved in his affairs.
You can call the police as a concerned citizen if you see them trespassing on your neighbor's land, and you know for a fact they don't have permission to be there. In fact, it would be a good thing if there were police reports establishing the trespassing had occurred in case anything happened, like property came up missing or he was harmed in any way. Cops like it when you let them know what's going on, even if they can't write any tickets on the spot. It gives them something to put in a report, that way they have a heads up on the situation if they ever get called out for anything more serious. Just be sure to use your department's non emergency line. It's also a chance for you to get to know the local officers, which is always a good thing.
Also, if it ever develops into anything more serious, your police reports might go a long ways to convincing a judge to issue a restraining order. Just in general, there will be more to prosecute if there's an established history of documented property crimes leading up to anything serious. It might even give the local officers probable cause if something comes up missing, or at least motivate them to pursue it more aggressively. I believe it would also be legal for you to video them trespassing, as long as it doesn't lead to you trespassing in the process. If you can clearly see the activity from your own property, I'm pretty sure it's legal for you to film it and have it admissible as evidence.
Another thing you can do is establish a neighborhood watch. If anyone sees any trespassing or suspicious activity on anyone else's property, then they just call the police and file a report.
But before you get carried away, what exactly are these guys doing that makes them "bad guys?" It sounds like they're just taking a short cut. I could see if they were loitering on your property drinking beer and vandalizing stuff, but what is so threatening about them simply cutting across your yard? Are they intoxicated? Have they shown any tendency to be violent? Do you know for a fact that they've stolen anything from you? I understand not wanting people in your yard, but it seems they've respected your wishes.
How exactly do you know that your neighbor told them off? You can't be certain that what he tells you is the same thing he told them. For all you know they have some kind of agreement and he just tells you what you want to hear to get you off his case. Maybe he doesn't mind them cutting across his yard. Depending on the circumstances, I wouldn't. Before you insert yourself into this situation I would make certain there's even a situation in the first place. I think it would be a lot like getting involved in a domestic dispute. You think you're rushing to someone's aid, only to find yourself the sworn enemy of both parties. This could very well end with your neighbor pissed off that you got into his business, and it might end up with them allied against you. Honestly, if he's all there mentally I would probably just stay out of it.
ETA: If you really feel responsible for this guy, just put up a surveillance camera. That way if anything does happen you will have it on video, and he will be thankful for it. Best of all, it doesn't require you getting involved until something actually happens. That way you don't become "that guy" in your neighborhood.