Mystery of Mamo - Well, it's a required taste; some will enjoy it and others won't. It's pretty dark and very surreal but has a lot of awesome moments. Zenigata trying to kill Lupin rather than just arresting him might leave you with a bad aftertaste. If that wasn't bad enough, he doesn't even necessarily want to do Lupin in by himself; at one point, a giant truck tries to run the gang over and Zenigata cheers the driver on. Shamefur dispray.
Castle of Cagliostro - I think it's the best one, but it's not my favourite. It's more Miyazaki than Lupin. So while Cagliostro is great, it would probably not make a good starting point. The plot is awesome, so is the music and I especially liked Lupin and Jigen goofing around in the intro. It also has one of the best villain death scenes in animation.
Farewell to Nostradamus - The fans are definitely too harsh on this one. I thought the political aspects were silly, but I liked the rest of it for the most part. I'm confused on who the "uncle" guy was though.
Dead or Alive - The darker art style is enjoyable; Goemon also gets more screentime than usual and Fujiko less which I'm completely okay with. One might even argue that she's not the primary love interest. Zenigata is more competent than usual so that's cool.
Episode 0: First Contact - Masterpiece; my favorite.
Lupin III vs. Detective Conan - Much more Conan than Lupin. I'd like to see more crossovers though.
Blood Seal ~ Eternal Mermaid - Even by Lupin standards, the villain is ridiculous is this one. The plot is predictable and generic, but it has some awesome remixes of the main theme and like someone pointed out, it was nice seeing grandpa Lupin in flashbacks.