to answer a couple of the questions...
I use anapod explorer, made by redchair...the same people that make notmad explorer. I've honestly never used itunes, but the whole interface seems clunky to me. Anapod explorer is very neat and keeps things very tidy. It allows me to upload vids, photos, and mp3s by just drag/dropping. With the ipod video, you can do album art too, which it can download from amazon for you if you'd like. I use Tag & Rename too, for tagging. When I do that it makes an album art file in the folder with the files - folder.jpg. Anapod Explorer will automatically associate that with the mp3s. You can also drag in any picture to associate with files. So if its live stuff, you can still have a picture there. Ok, ok, so you don't really need album art, but I still think it looks cool, and its easy as hell to add.
I also have sharepod installed so i can use my ipod on any computer and access its files. no need to install itunes or whatever on the computer, sharepod runs right off the ipod.
I wanted to go video, not that i'd use it all that much, but still the option is nice. Theres nice programs out there that convert the video (divx, xvid, dvd, etc) to ipod video. I know some other mp3/video players can play the divx, xvid, etc files without the conversion, but i've also read that they don't always work and sometimes there are sync issues.
As for accessories. The ipod comes with earbuds, a cheap leathery slip cover, and the usb cable. I had to buy a car charger and wall charger. I didn't really need these, but I found them on the net for $5 shipped. Not bad at all. I also bought a nice clear plastic cover for it with belt clip and whatnot for around $10. That way the ipod stays finger print free and safe and secure.
as for flac...i think they have the 3rd generation ipods running linux, i think they're still working on the 4th and 5th ones. Within linux the ipod opens up even more and they are working on flac support. so theres hope. plus if you install linux, you can still dual boot or whatever, and have the option of going to the normal ipod bios or the linux bios at startup. Eventhough the ipod video isn't implemented in all the fun yet, it will be in time.
overall though, the ipod has the best form factor and looks the slickest out of all the ones i looked at. and its small as hell. as for the car, my receiver has an aux in on the front that works perfect for all of my needs.