A few days of using the iPod later...
I've ended up installing iTunes (the bloated tub of lard it is) because it handles Video, Podcasts and Audio books better than WMP11 and DOPISP does (i.e. you don't get track 10 from the Czech CD while listening on random

) and have let it resynch my library - so I'm now more of a "proper" ipod user. In some ways the iPod and iTunes are better than the Zen/WMP 11 combo, in other ways they are worse.
Firstly the iPod is easy to use, at the expense of lacking features (or at the least having no obvious ways of accessing features!) - although I will admit tacking some time to work out how to change the damn volume on it!
On the other hand iTunes is annoying + and - don't expand drop downs like they do in every other tree like menu, and it's generally keyboard unfriendly (I usually find it quicker and easier to use the keyboard vs the mouse/trackpad)
Firstly a couple of things I miss from the Zen are...
The context menus while playing songs - i.e. If I was listening to my "Rock Tunage" playlist and a song by Fall Out Boy came on I could decided to "right click" and select "Lookup Artist" and then select the "From Under the Cork Tree" album, and either listen to it or append it to the queue - where as on the iPod I have to navigate though all the menus to find it.
Another thing I miss was the ability to "right click" on a track and find out further info about it - primarily the year of release - I can't settle pub arguments as easy now
iTunes doesn't appear to have a way of monitoring folders, due to my syncing to a NAS for backup and sharing between three PCs tracks are not always added on the machine my MP3 syncs though so this is really annoying.
Now getting onto some more positive things :-
I'll start with the poorest implemented nice feature -
Audiobooks - urgh; Nice that it separates them out the core library, but why does it play them one by one? I have a single "Audiobook" at present (Which i've had to convert from MP3 to M4B format, but hey I wanted it out the way!) but can I play it though in one go (like I can with the original CD) - can I **** - In fact it's listed as 10 different books - argh!
Podcasts - Ooooh; Now this is how the Audiobook menu should be structured - again they are kept out the main music collection, but this time they are separated into different programmes/feeds (whatever) then listed in reverse order. The iTunes interface to them is great too. So far I can't fault the Podcast feature at all (well aside from iTunes not realising MP3's with the genré tag of "Podcast" are Podcasts but hey I only had two).
TV Shows - Ooooh; this works nicely (similar to Podcasts) - shame iTunes can't a) Monitor Folders, b) Convert without losing sound (Videora gets round that one but is a swine to use), c) "hide" the original file in the library when converted.....
Music Videos - Back to a more "Audiobooks" style menu, again all get dumped into a single list - why not display "albums" in sub folders? (Also see TV Shows comments)., doesn't appear to start playing the next video when the first finishes.
Movies - ROTFLOL, Who's going to watch a movie on an iPod? No idea how it works as I can't see a use for this feature.
Music Library - Firstly no chance of accidentally hearing a Podcast or Audiobook as they have been separated out which is neat.
Coverflow is cool, if a little bit unresponsive
It's a pain selecting "The Zutons" as you have to scroll through the whole list; actually "The Zutons" is just time consuming, moving to something in the middle like "The Manic Street Preachers" is a pain - occasionally a letter picker thing pops up on screen, and suddenly dumps me on The Zutons - still can't work out how to trigger this or indeed work out how to "wrap-around" either (i.e. go from The Zutons to ABC)
Gapless Playback - urgh, why the need for two seconds of silence between each file? My Zen Touch, Zen Vision M and even my mobile handle that one fine, but iTunes has to faff with your library for hours to work that out (track 903 of around 9,000 at present

) - why not just play the MP3s with no bloody gaps? All the CD's I've ripped have silence at the end of non-gapless album tracks anyway
Audio Quality - Is fine, my earlier concerns were down to the iTrip and Mobile. Speaking of the iTrip - works well in the car and much tidier than the Tunecast, not quite as clean as DAB, but less hissy than everything except Trent FM/BBC Radio Nottingham in the car.
The Dock Connector - I can see this is going to be neat when I come to replacing my audio and video equipment - no trying to fish wires down from the back of the hi-fi any more - I have already brought an iPod Speaker/Dock (on offer at Richer Sounds - £20 with a voucher from the local paper

) - literally drop the iPod to play and charge - no messy wires hanging out the player - I know my brother also likes being able to control it from his in-car head unit while it's charging.
Last FM - The syncing of play counts between iPod and iTunes means my Last FM page is going to finally represent more of what I actually listen to, rather than the randomness I have at home - requires a systray plugin though which is a bit messier than the WMP one.
Going back to my original post - I'd forgotten I had ~9,000 tracks as they didn't fit on the Zen - it's great having the capacity again. The Search really is neat, and the speed hasn't changed at all.
And the most irritating thing of all - forgetting which playlist I was listening to when I connected to my laptop - I just want to select "Now Playing" to get going again.
All in all the Zen V:M and iPod are on par - they both have their own strengths and weaknesses.