I still think Twin Peaks is the best show ever created but I have to admit that Lost comes really close (and 24 isn't too far either). Or actually I don't know whether Twin Peaks stands on it's own against all the newer tv-series with higher production values as what I like in Twin Peaks is the whole package: the books, the tapes, the movie, the series, the scripts. Those things together makes the world of Twin Peaks absolutely fascinating but when looking at the series at it's own, there is a lot of stuff that isn't as great as it should be. Even some of the highly acclaimed first season is slow and uninteresting. I like the intentional "slowness" in some of the scenes but, for example, everything about the Packard sawmill is quite boring in the first season (although in the finale of the first season it starts to get a bit more interesting, I finally got interested in that story when Andrew arrived).
Comparing to Lost and other newer series to Twin Peaks I can't deny the fact that the production team has the equipment and is more capable on doing things that can hold the viewers attention much longer than most of the shows in the 70s, 80s and 90s could do. They know better what strings to pull. I know that some of the modern series overuse (and misuse) the tricks and make it hard to watch but especially with Lost and 24 that is not the case.
I actually didn't care much about Lost and 24 when they first began. I started to follow 24 when it's 4th season was aired and I did watch Lost from the beginning but didn't like that much it's first season. The second season grabbed my attention immediately and after seeing the 2nd and the 3rd seasons I'd really like to see the 1st season again.
The difference between the mysteries in Twin Peaks and Lost is that on TP the best things were laid out more intuitively whereas Lost has done it more purposefully. There are things in the beginning of Twin Peaks that were done without knowing what they mean but what starts to make sense later in the series. In Lost, there are things brought up in the first season that don't have an answer yet but, according to the creators, were made with a thought-out purpose and will be explained before the end of the series. Both styles can be honored. I takes a certain something for a man to be able to create something from his subconscious and it's also amazing to be able to think the whole thing through and start bringing these things up so that in the end it all makes sense.
Twin Peaks is disturbing and doesn't apologize what it shows. Same could be said about Lost too. They could do things easy for the viewer and let every good people live and every death to be mild and mellow but so far we've seen several very surprising deaths of characters we didn't expect dying, or at least not so soon and we've even been shown two people being buried alive (I was so sure that they wouldn't pull that off but damn it, they did!)
It has also helped Lost that they've been open about the fact that it is going to end and they've even given us the number of seasons it takes to tell the story. Twin Peaks was meant to be going and going and going. The viewers might've been thinking that the weird things are too much especially when they are not going to be sure if those things will be explained at all. In the case of Lost, people know that the answers will be given eventually. On the other hand, much of the greatness of Twin Peaks comes from the fact that they didn't manage to give up the answers. Explaining things in the end might cost a lot for Lost but it's also possible that they'll be more vague with the answers by telling us just enough and not too much.