PUGging into 25 man raids
While it's easy to pug into 25-man Naxx, Vault, and Obsidian Sanctum, it can be considerably more difficult to pug into the current endgame. Before you queue up, make sure that the members of your team that you take with you are familiar with the fight mechanics. If you've been running the 10-man version you should have a pretty good idea of what to expect. Take the time to brush up on the differences between ten and twenty-five man.
In many cases you may find yourself in a raid that's not quite up to the challenge. You may be saved into a raid with just a few or no bosses downed at all. Then again, you may PUG into a successful raid with experienced raiders. This is a great opportunity to learn more about the mechanics of the fight, and possibly get some great gear. On the subject of gear, make sure you know how loot is to be distributed before you enter the instance.
Remember, that you are guests of the raid. You'll find sometimes that the group you're in might do things differently from your guild. Just go with it and enjoy the raid.
Running guild 25-mans and PUGging empty spots
If you're close to a full 25 man, but not quite there, you might want to run the raid and invite friends and PUGs along. This is a great opportunity for gearing up your guildies and making friends on the server. Even if your guild is small you can gain respect on your server if you perform well. Make sure your loot rules are clear at the beginning of the run. Though it's painful to pass gear to non-guildies in this situation, it is only fair.
There are a couple of downsides to this of course. Sometimes it can be time consuming to fill up a PUG group, some folks may get frustrated with the wait. Since PUGs have little investment in the guild they may not be patient and leave the raid even before you get started. If you PUG in someone that you don't know you may get someone who's not quite ready for the raid. Even if you check gear scores, there's little guarantee that they have the appropriate skills for the raid.
In this scenario, you are the host. Be mindful of your guests and make sure that they feel welcome and valued. You never know when you may need them to fill in again.
Running with another guild
What do you get when you combine two ten-man raid guilds? A 25-man raid! (at least in theory) There may be another guild on your server in a similar position to the one yours is in. The advantage of this scenario is that you can run with the same people and learn their strengths and weaknesses. You can be fairly confident that your raid will proceed without worrying about PUGs.
Of course, this isn't a perfect solution. Loot is probably the biggest issue. Both guilds must agree on a fair loot system. Sometimes this can lead to an "us vs. them" mentality. Remember to be firm, fair, and consistent with looting rules. Purple pixels are not worth burning relationships over.
Remember that there is only one raid leader. The teams need to work together and maintain congeniality. At some point, you may merge, you may not.
Be content with 10-man content
Blizzard has actually been making some strides toward making a true 10-man progression. With the most recent patch, guilds geared in 10-man Ulduar gear can readily defeat the Trial of the Crusader on 10-man mode. Guilds can also progress by doing hard-mode fights and harder content. Smaller raids are more enjoyable for some and easier to keep moving along.
Remember though, that your guildies may not be content with just running 10s. The larger raid content still gives a higher level of loot. While smaller runs are less like herding cats than the larger ones are, there is more prestige attached to 25-man raiding. You may lose members to larger guild.
If you're raiding solely for the love of raiding and progression, this might be the best option for you.
In the end, make sure that you talk with your officers and guildies about what the best option might be. Hang in there, and don't get frustrated.
WoW.com offers a plethora of information on guild leadership and guild membership. Be sure to check out Scott Andrew's Weekly Column Officer's Quarters and keep an eye on the community with Mike Schramm's Guildwatch.