It depends on how you look at it. Musically, it's really easy:
Old School: WDADU - FII (All these albums sound like young guys playing music because... they were young guys playing music)
Rudess Enters: SFaM - 8vm (The DT sound is honed in with Rudess added. Instrumental breaks, heaviness, crazy experiments, and so on)
Signing with Roadrunner: SC - BCSL (DT becomes an institution. All the success is there, and they get heavier and darker to keep up with the times)
Mangini Enters: ADTOE (Portnoy leaves, DT has to rebuild)
But in a broader sense, well, it depends on how you look at it. DT's made a major shift in some way with almost every album. But if you want to look at the eras in terms of their careers, I think there's only one way to do it.
Breaking in: WDADU - I&W
Struggles and Success: Awake - SFaM
Building the DT Brand: 6DOIT - 8vm
Roadrunner: SC - BCSL
Mangini: ADTOE
And here's why I think it works. Even though they had gotten LaBrie and signed a new record deal after WDADU, DT didn't become a valuable property to anyone (including themselves), until Pull Me Under hit.
From there, the next three albums were a constant struggle. KM leaves, the record label interferes with FII, DS is fired, MP almost leaves (unlike now, this might have sunk them), they bring in Jordan and hope that Scenes will succeed.
People think of Rudess joining the band as the beginning of a new era, but that's not really true. If Scenes hadn't succeeded, their careers might have been irrevocably destroyed after FII cost them so much credibility. Two flops in a row? Very, very bad. The success of Scenes was what transformed their careers. They got complete creative freedom and solidified the fanbase's trust in them.*
The next three albums were more or less an effort to maintain that success. Now that they had a legitimate dedicated fan base and the creative freedom to maintain it, DT's relations with the fans and the expectations of their music were created. Evening With shows, increased internet presence and experimentation with the music within a specific style which allows you to go from Blind Faith to As I Am to I Walk Beside you without giving the fans a sense of whiplash. Then the Atlantic contract runs out, Score is made, an era ends.
What's strange here is this is where the musical and career eras converge. Falling Into Infinity was made under completely different circumstances than Awake, and the music shows it, but fundamentally it's still guys in their 20's making music. Different place in their careers, but the music still spoke of youth.
Once they started with Systematic Chaos, they were in a place where their careers were doing amazingly and the music reflects that level of comfort. SC, based on the CiP documentary, was basically made without any real distress. Black Clouds reflected the necessary career/business move of making a "DT" album rather than an album with a specific focus like SFaM (concept album), 6DOIT (experimental album), ToT (dark and heavy), 8vm (pop/prog), SC (balls). Business and art merged.
And then Portnoy left, which again blew up everything. It's still hard to put this era into context without hearing the album, but we can say for certain we're in the middle of a seismic shift in DT history.
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*In retrospect, it's amazing how much pressure was put on Rudess. Mangini has big shoes to fill, but JP/JR/JM/JLB have done everything possible to take care of him and ease him into the band and the fan base. Rudess had to come in and reinvent DT's keyboard style for the second time in two albums, and if he failed the band might have sunk. Aside from being in the band for over a decade, I can see why Rudess so obviously carries himself as "the" DT keyboardist. He's as much a part of what DT is today as JP/JM/JLB. Mangini hasn't had this moment yet, it will be interesting to see if he does.