I'm split down the middle on this one... The '90's did have some memorable Trek literature, and with it's 'episodic' nature, the novels are much more accessible to a casual reader, as I was back in those days. The downside to that, though, was that Sturgeon's Law was in full effect back then, and the majority of stuff written was somewhat... forgettable... the main exceptions for me being just about everything written by Peter David, Diane Carey, Greg Cox, and Diane Duane, with a few isolated novels here and there capturing my interest.
The 2000's, though, have created a different breed of novel. Without network oversight and an active series to restrain it, it's allowed a new breed of writer to take a different spin on the Expanded Universe. The quality is by far much more consistent, now, with much more consideration of the questions that always bugged me about all the series, as well as really weaving them together into a cohesive unit that totally failed to happen with other EU fandoms (*ahem* Star Wars *ahem*). It's essentially distilled what I like the most about the '90's novels and refined them even further. I even remember when I first noticed this new trend: After walking away from the fandom for a few years, my eye was caught by Ex Machnia. I had recently rewatched ST:TMP and was fascinated by the attempt to follow up on the implications of the V'Ger encounter, written by a (at this time, to me) unknown named Christopher Bennett...
Quite simply, I was blown away. While expecting just a bit of fluff and maybe a bit of continuity porn, I got a fairly deep story that touched on modern day issues without being totally anvilicous about it but without losing that Trek magic, as well as, yes, giving me quite a helping of continuity porn to boot... This brought me back to the novels again, and I've been a faithful follower ever since...
So all in all, I'd say right now is my favorite decade... The writing is great, considerate of the fans, and, most importantly, is more consistent and cohesive than it's ever been before, to the point that it's better plotted than the live action series were, in point of fact. If Paramount ever decides to do another TV series, they would be severely remiss if they don't sign on some of these authors for the project....
But the '90's will always have a special place in my heart...