[nitrous9200]

That's a HUGE list, maybe you could sort them out further so it's easier to digest.
A few essential things like ICS and .Net 3.5 are unneeded if you use a custom ROM as they are already baked in. Many of the other apps like Google Maps and Bing are built into those as well. Flash isn't necessary to install, Opera has it built it (at least the way I've got it setup) but it doesn't play much except YouTube, and even then it's slow. Might as well use the official YouTube player, which is great.
Currently I'm using a Windows 6.5 rom as many of us are, and it has the new "Titanium" panels interface. I like it a lot and being built into the software, there is nothing to load and works very well.
I personally don't like the S2 apps, I think they're ugly and I didn't buy my Omnia because I wanted it to look like an iPhone.
My Mobiler is useful to have but it isn't even working in 6.5.
ClearTemp can actually free up a decent amount of space from assorted applications but I usually flash/clear out My Storage a lot so I don't worry about it.
There is a cab on here and on XDA-Developers that will shut off your broadband after 1 or 5 minutes. All it does it make a registry edit that you could do on your own if you wanted. Speaking of which, PHM RegEdit is a good but non-fingerfriendly editor on the phone directly. CeRegEditor is PC based, you connect to ActiveSync and it will allow you to edit your Omnia's registry on your computer (much easier than doing it on the phone).
Caxixi and Midomi are very fun/useful but I haven't fired either one up in a while.
My most commonly used apps are Facebook, Pandora and YouTube. Facebook may be limited but it's only version 1, I'm sure it will get more features eventually.