Windows ME was my most disliked OS (too buggy, even after service packs). I think the level of complexity finally hit the wall given the 9x series lack of good memory/file protections.
My favorite 9x OS is 98 SE (which was a stand-alone release, not a service pack). But 98 "first edition" did add substantial features to 95: IE 4, multi-monitor support, sfc was added (which was useful because 9x got corrupted a LOT), ACPI support, better plug and play, and better hardware support overall.
98 SE just added USB support out of the box (which was a big deal for those of us trying to use USB mice), IE 5, WebDAV, Windows Explorer improvements, ICS, improved WMP, and all of 98 "first editions" hotfixes and updates. You could make 98 "first edition" into 98 SE more or less, but 98 SE was a nice thing to "just install" and have everything work.
My 1990s/early 2000s OSs looked like this: 3.1, 95, 98, 98 SE, ME, back to 98 SE, and then 2000, XP SP1, and beyond. Skipped XP pre-SP1 as it was a pretty shoddy release compared to 2000 at the time, and ran away from ME screaming.
I ran all of those windows versions as well, but my favorite remains NT4. I stuck with that for a long time, until the lack of drivers forced an upgrade. It was incredibly fast (smooth on a 66 mhz 486), rock-solid (uptimes of weeks with daily use), light-weight (32 MB RAM was doable, 128 MB was multi-tasking heaven). It's nice that MS is trimming down windows lately, but I keep thinking that it's a bit like seeing someone who has let themselves go get back on a diet. If they hadn't put on the weight in the first place, they would have never needed to lose it.
Dos6+Win 3.11, OS/2 2 and 3, Win98se were the best, XPsp3 as well. Win ME had one good thing going for it: window transparancy and alpha blending! For that reason I used it with a HMD, backstrapped laptop and webcam.
Awesome project though!