The only thing holding back a second group is leadership.

If you're like many guilds with one autocratic GM, 2 groups is going to fail miserably. Many, many guilds have a deep lack of leadership outside of the GM/Raidleader. There really is a certain amount of chemistry that these kinds of people bring out in a raid, and finding that with a second person is going to be extremely difficult for most people. You may find your raid not even listening to the second guy. Its really akin to a substitute teacher effect - not much learning is going to be going on that day.

Maybe if you were seperated by schedule, but even then, a lot of people are flexible enough that they'd just migrate to the "better" raid.

(In the end, I expect that TBC will result in the 3 top-tier guilds on my server sloughing themselves down to 25 man size, and a 4th guild forming at the same tier of content in the process. I don't necessarily mean sloughing as in "You're cut" but as in people who've been discontent with something - schedule, leadership, raid slot availability, etc. - leaving in the same time frame and naturally falling into a new guild. Most of us get along between the 3 guilds, so it wouldn't be totally unexpected.)

As a raid leader of Goon Squad, it is very interesting to me to see the issues of multiple raid groups discussed. In a sense the issues people are beginning to imagine the expansion will bring, are issues that we have been struggling with since day one.

I currently have 1160 unique accounts listed in our out of game database (blizzard in game db breaks after 500), more than half of them actively play today. Last week we had 242 players attend at least one Goon Squad 40 man raid. We have tried many different strategies for dividing people among groups. I will note and discuss a few of them here.

Managing multiple groups adds an extra layer of administration to end game raiding. The administration of player attitudes and perceptions. One player's DPS can double just by moving them into a group that they think will succeed, rather than a group they think will fail. Dealing with this is hellish.

Common group types

Unequal A team / B team / C team
This method puts your star players in the A team, and tell the rest to play their best in the B team while they wait for spots in the A team to open. Given the current style of blizzard raiding content, this is probably the best option if you are concerned solely with progression, at the expense of your members. This has your B team guys essentially gearing up as best they can waiting to be poached off by the A team as they need members. Terrible drama results, expect the B team attrition rate to be high.

Random Equal A team / B team / C team
This involves a mass signup with raid leaders dividing out balanced groups. This is generally worse for progression since you need to split up your leaders, your tanks. Maintaining the equality of the groups is terribly difficult. People are raiding with a different group each week essentially, it is tough to get a cohesive atmosphere. You get hung up on little differences in the way each group does things. Partially through the raid, oh damn I am in the other groups healing channel. People trying to manipulate the groups for better dkp standings. This setup also is precariously balanced, and without top notch trusted leadership managing the balance can easily slip into an Unequal A team / B team setup.

Fixed Equal A team / B team / C team
Guilds within guilds essentially. Fixed groups that dont have the option to move from the B team to the A team. Therefore since you are stuck with your group you might as well make the best of it. Avoids a lot of the balancing problems and underperformance problems of random/equal teams. Causes many problems as well. The egos between groups make it very difficult to trade players around to fix class balance/ sharding loot. Attrition hits this type of setup very hard. People don't want to leave their groups, essentially each group recruits from outside furthering the notion of separate guilds with one tag. Guild leader favoritism between groups can become a problem. Every decision that gets made will screw some group over in their eyes. People who do attend other groups are accused of "stealing loot." [from their own guildmates]

A team only
Have one team working on unconquered instances. And only once your best with the place to farm status do you slowly teach the rest in a much more stable learning environment than wiping with a subpar B-team. In my opinion this is the best option. It leaves a lot of people out in the cold though, especially in guilds where there are far too many skilled players for 1 team. Forcing people to not form up a B-team for the "good of the guild" to avoid the B-team problems just doesn't sit well with most raiders. Neither does simply not being able to raid.
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Attitude Juggling

A-Group attitudes
A groups require constant performance evaluations, especially if they have well defined posted rosters. Once you make it to the A team unless leadership makes it clear that you could just as easily be kicked off, performance tends to drop off as people are comfortable with their cushy guaranteed A team spots.

B-Group attitudes
B groups tend to take on one of two attitudes. Either the I am in the B group, this sucks, I am not going to even try attitude, or the "they say we are the B group, lets show them who is really the B group" attitude.

The former tends to lead to a stagnating, underperforming B group that continues to fulfill its own prophecy of mediocrity and results in horrible morale and frequent quitting.

The later can frequently drive the previously undergeared/underexperienced guys relegated to the B-group with such energy (sometimes bordering on rage) that they will burn through content by simply outplaying it in a rabid attempt to "beat" the A group. Usually once this is done you are left with two groups that work well with their own members, but are highly suspicious of the motives of any member from any other group approaching "their" accomplishments. This tends to lead to Fixed A team / B team setups unless dealt with quickly by leadership.

Key notes with multiple groups:
As previously noted, presence of the previous / known leaders flat out improves morale and performance. Any raid with the guild leader in it usually does better. If your guild has multiple known leadership figure heads try to split them up between groups. If you don't ouch.

The decision of how the groups are created, no matter how the decision is made, be it fixed baselines, officer discretion, random split or whatever will be met with suspicion in all but the most tight knit groups. People will pull patterns out of nowhere (think blizzard forums discussions of random) and "prove" that the groups are unfair.

Group making is an easy scapegoat for failure and lack of progress "we were put in the crappy group, this sucks" rather than "we screwed up lets do this better." A guildmate of mine described this well after a bad night for two groups saying "As long as we all failed its OK"

In general, running multiple high end groups working on the same content within a guild is simply a bad idea. Unless you have some other outside force (other than desire for progression) that unites the members of your guild (be it an out of game situation, or just the relationships built from 2 years of raiding with the same 40 guys) you are really better off as separate guilds. If you do have that something that binds your guys together, something worth giving up a bit of progression for, then it just sucks.

That said, TBC may also open a few doors for certain people and guild types. Particularly in regards to time zone based groups helping with scheduling, as well as giving people who don't quite enjoy raiding as much as they appear to a chance to take a break.