My point was that the content defines "good enough". You are right that you can select the guild. However the selection goes for content and not for effort. Effort is defined by content.
This is true to a degree. But I think it's still a good idea to farm and exceed content requirements for several reasons:
1. Future Content
We are not just gearing for the current fight, we are gearing for future fights. Sure, if Patchwerk only requires 2.5K DPS, you're fine. But what do you do when the next fight requires 5K DPS? If you prepare beforehand, you're golden. Otherwise, you have to work on getting the required gear instead of trying the fight you really want to do.
The moment Ulduar comes out, we're going to drop Naxx like a hot potato and dive straight in.
2. More Options
If your gear exceeds requirements, it gives you more flexibility. You can do easy encounters or hard encounters as you choose. You can bring alts, because the mains can handle it. You can let a healer attempt to DPS Scions of Eternity for an Achievement, instead of needing her to heal 100% of the time.
It's like having a lot of gold. You don't need 50K gold. Personally, aside from buying my Epic flying, I've never exceeded 5K gold at any one time. But having more gold on hand makes life easier, because it gives you more options.
Additionally, it also gives you flexibility in recruiting. If a portion of your raid exceeds minimums, it allows you recruit good under-geared players and gear them up without having to go back and farm old content.
3. Greater Margin
Better gear reduces the probability of a catastrophic mistake. If you kill a boss in 5 minutes instead of 10, it's less likely that someone will make a mistake which causes a wipe.
As well, better gear allows you to be successful with less skill. Yes, Ensidia and the other top 10 guilds can probably blow through content with minimum gear requirements. But most of us are not Ensidia. If my time-on-target is 10% less than an Ensidia rogue--because she's better at movement--I'm going to need to hit 11% harder in order to do the same damage.
4. Raids are More Fun
Most of us raid because we enjoy raiding. But honestly, wiping on content we've already beaten is not fun at all. A high degree of effort leads to faster, cleaner raids which is more fun for everyone.
Wipes also increase the effort required. For example, my guild uses Food+Flask on all our Naxx runs, even though we probably don't need to. But wiping incurs repair costs and wastes time. The Food+Flask contributes to a faster run with a minimum of additional costs.
5. Expectation Management
If you expect more from people, they will respond to that, and rise to the challenge. If you expect the bare minimum, then the minimum is all they will give you.
Maybe Food+Flask is unnecessary. But it is a signal to the raid that you are willing to give 100% on this attempt. That you are willing to incur a cost, maybe even just a symbolic cost, to ensure success.
I think people respond to that, mirror the group they find themselves in. If you're in a raid where people slack off, often you will start to slack off as well. If you're in a raid which has high expectations, often you will rise to meet those expectations.
The most important part is to have the entire raid on the same page as to what "good enough" means. But there are significant advantages to having a higher standard of "good enough" than is strictly required for content.
However, it's also possible to take this too far, especially when looking at new content. By far the most important element in mastering new content is spending time on it, not gearing up for it. If Ulduar comes out, and you decide to spend a few weeks farming Kel'Thuzad instead of trying new bosses, you are making a mistake. But having a raid that chose to exceed the minimum requirements back in Naxx will help you greatly in Ulduar.