Wouldn't say that anime was in general better in the 90s as much as it's a lot easier to watch all the crap that's released now, whereas back in the 90s, getting anime was legitimately difficult. My guess is just as much crap was released back then, but Americans just had a smaller sample size to draw from. But who knows, I find cartoons in the 90s to be much more entertaining than cartoons today.
For me, anime started sucking horribly right around when Haruhi came out, causing the moe movement to boom out of control. Mind you, this happened about 1 year after I started watching anime. What it comes down to is that 90% of everything is crud (Sturgeon's law) and eventually one becomes disillusioned to it, sooner or later. With anime, and pretty much every other media form, it is because everything is recycled, and eventually you'll have seen it all and nothing will be feel as fresh as the first thing you saw because they are all imitations rather than products of original inspiration. Haruhiism just kicked the recycling into a gear never reached before due to how awesome a phenomenon it was, and how easy it was to market moe for big money.
That being said, 10% of everything is still pretty good, and there are shows that are still entertaining. Just means that I spend less time watching all the crap, and spend more time looking for that 10% of goodness. But I digress.
in no particular order:
R.O.D. OVA
AIR (first two arcs are slow and confusing for some, but the last two arcs are in my opinion the best story telling anime has to offer); in a related vein, Clannad, Kanon. Some people like these shows, some people don't, but in my general experience most people liked Air.
Nana
Toradora!
Angel Beats!
Working!! (haven't finished watching this, but it's quite frankly this and Angel Beats! are the best comedies I've seen in a very, very long time)
Focus on newer stuff, as older works have already been discussed to death, but special mention to Azumanga Daioh which I just assume that everyone who has watched anime has already seen.
And shows that I just found extremely entertaining, but hardly consider must see, guess Working!! would go here normally as I don't rate comedy that much, but w/e.
Beck, Nodame Cantabile
Nanoha
Saki
Could go on forever about shows I just like, but this is probably a sufficient sample.
