I prefer Joel, not necessarily because of his hosting, but because when he was hosting, the whole team was together. Mike was the head writer even from the beginning, so he was always there, but once Joel left, it was like a piece of the show had died. In later seasons when more and more of the original cast had quit (mostly due to CC and/or SFC interference) I found that the show just wasn't the same.

For me, the 3rd and 4th seasons are the best. There are plenty of awesome Mike episodes, but those seasons are the Golden Age to me.

For more modern things, you have RiffTrax, which is Mike and a few others riffing on big-budget movies. It's interesting, but mostly they're riffing on movies that are actually good (at least compared to normal MST fare) so it loses some of the magic. Unless it's a big-budget movie that's actually bad, in which case it's amazing. Some of them, like the ones for the original Star Wars movies, have almost no riffing at all, it's more like fanboy-gasms.

On the other hand, you have Cinematic Titanic, which is Joel and basically all of the original cast except for Mike, riffing on bad movies like the good old days. I haven't actually watched any of these, but apparently they're pretty good.