"Well, it's good to check the alternatives. I'm not really committed to any brand and since both the Naos 5000 and 3200 are quite old models and my experience with their software perhaps isn't the best I figured I'd see what some other brands have to offer."
I wouldn't worry about their age. The Naos 3200 still has what many out there to be the best current mouse sensor in the marketplace. The only difference in performance between different mice with the same sensor is how the company implements it through firmware, and lens placement. This is why we usually hear the top three current models in the market to be the Zowie FK, Razer Deathadder, and Logitech g400s. The other mice with the Avago ADNS-3090 are not quite as well implemented as those top three. Will this difference affect most people out there? I doubt it. Yet, people like making definitive lists and this is the result. I'm no better with my g400s than I am with my CM Storm Recon. I only use the g400s because it is more palm grip friendly than the claw style of the CM Storm Recon.
"Can't say much about the Zowie else than that it looks very generic and not too ergonomic at first impression. Does it offer any special features like programmable buttons?"
Compared to your Naos, others will be less ergonomic. The only other mouse I can remember off hand that is similar in shape is the Func MS-3. One came out before the other, I can't remember which. Either way, those are some very comfortable mice.
Zowie is known for their minimalistic approach, putting performance above all else. Forgoing software and customizing, for predictability with plugging it into various computers other than your main one you game on at home. The ec-1 is comfortable though, it's like a larger intellimouse style shape.
"The Roccat model looks neat, although I see a bit of mixed reviews about it."
Roccat is a very underrated company, and is still fairly new in the North American market. They are German I believe. They make my favorite mice mats so far, the Taitos. That being said, I've never used anything else in their product range unfortunately.
That being said, I find mixed reviews on nearly everything really. Engineering in general, and of course including mice, is a set of compromises. Perfection doesn't exist, and what we call perfect is simply a subjective viewpoint from an individual. Something that I absolutely rate highly might not be suitable or liked by someone else, and vice verse.
So far though, i don't have any reason to think their mice are low quality, or cheaply made. You didn't state any complaints from those mixed reviews so I can't say anything other than that.
"As for the Logitech g400/s.. Refer to my post about it."
Yes, I wasn't really suggesting it. Just commenting on my experience with it since it was brought up. I was talking more about what is palm grip sized in comparison to the g400s more than anything. On a further note, the g400s is very accurate, but the cord and mouse wheel annoy me constantly. Again, nothing is perfect... compromises, blah blah blah.
"I switch to another OS or plug it in to a different computer without the gaming software installed (and even if it is I'll have to copy over my settings to that computer and go through all that hassle in order for it to work)."
Zowie fans list this as a top reason to switch to Zowie mice. Then again (Compromises, no perfection, blah blah), you will be giving up macro's and customizability like changing led color. Their mind set, if I could sum it all up, is to try to get the options right the first time and keep that as default.
"I have no experience/information for other brands like Corsair, Steelseries, Razer, Roccat etc.. in this respect but if anyone knows if anyone else than Logitech requires you to install and run their driver software in order for it to run consistently (rather than revert to factory settings), let me know."
With my g400s I never installed any software. I've always heard reviewers, including Linus, say that logitech has the best software for mice. I personally haven't used every manufacturers software out there, so I don't know. I never had any issues with logitech, microsoft, razer, and CM storm mice software in the past. Didn't like the look and feel of the microsoft and razer versions but, thats just a subjective opinion on my part.