The best method? Allow multiple shells equipped at a time each with their own assignable /# channel. This allows you to have casual shells, event shells, and goal-driven shells (i.e. HNMs) all at the same time. It also allows for shell heirarchies for LS alliances.
In Aion there was an alliance on my server based around all of us belonging to a forum community. Despite this, there were various factions that formed different legions with more specific groups and communities. All the allied legions would use a single custom chat channel, but would belong to our individual legions. In my idea it could work as follows:
/1 ALLASHELL - overall shell for alla members
/2 FFXIEXPATS - alla posters that played FFXI
/3 WELIKEPIE - small group of RL friends that post on alla
/4 PIKKOFANCLUB - self explanatory.
All posters on this forum might be a member of ALLASHELL. The folks from FFXI might also carry the FFXIEXPATS shell, though some members of that shell might not have the ALLASHELL. One of the ALLASHELL members might have the WELIKEPIE shell too, but most don't. The PIKKOFANCLUB shell has members from all in various configurations. Regardless of what other shells you have, you'll be able to talk to and do stuff with zam posters as long as you have the ALLASHELL active in your linkshell menu while retaining the ability to remain in any of the other shells you have active as well, but only people with your shell active will be able to join in that particular community. In the Aion example I gave, we could use an alliance shell rather than a custom chat channel and retain the functionality without having an easily infiltrated chat channel to keep an eye on.
Another good example of this are the custom channels in WoW. On Lightbringer there was a channel called "Endgame" where many of the hardcores or old timers (i.e. been around since the server went up) would set up spur of the moment events regardless of guild affiliation. The problem was that the channel's moderation was constantly abused ... something that could be solved with multiple linkshell applications.
The downside of this would be linkshell identification (i.e. the color blob). Aion did this very well with user customizable guild emblems. I would love to see a similar feature be used in FFXIV (not happening) where you could select the emblem from a single active shell to be shown next to your name (minus the transparent parts) in place of the color blob. The legion emblems in Aion were a very visible identifier to show where your allegiances were. Imagine a dynamis run in FFXI but instead of all having on a dynapearl having each member with their visible primary shell logo displayed but still all being able to chat in dynashell chat. It would be like that. Apart from displayed logos, this could also be something else like a custom "minicape" design that complemented the armor like that shown in this picture http://www.aionsource.com/forum/attachments/legion-discussions/7417d1253279589-show-off-your-legion-emblem-thread-aion0017.jpg
(again ... not happening, but would be nice).
In such a system guild banks would be a nightmare and theft would be rampant (this is the case anyway, but this would probably increase the problem). The best solution I can think of is a guild bank that only the leader can access but all members can see. The guildmaster can flag certain items for distribution to a certain member, a certain rank, or as free for all (flagging can be done anywhere at any time, though items couldn't be added or removed). This would allow for disbursement if the GM is busy. In order to have access to a guild bank there must be a junior guildmaster established (and currently subscribing), however, so if the GM is banned or quits the junior GM can access the bank as full GM after, say, 14 days. No member may take more than a certain number of items (ideally calculated by value, though this is tricky and probably not doable) from the bank in a set time period including the GM to prevent looting and a majority vote of the shell at any time can cause the bank to become "locked" preventing further looting. This is all pie in the sky, though ... guild banks are always going to be a nightmare except in the most tightknit groups.
A better rank system also needs to be put into play as well so you can better utilize the guild bank, any "guild leves" that might be in game, chat permissions, or for invites. Invites always angered me in FFXI because sometimes you couldn't get an officer to a new member and had to sack a junior member (or one that wasn't too trustworthy) so they could do the job. At the very least let us mail pearls!
It would also be nice if there were shell bonuses. Lets give an psuedo-FFXI example assuming we could use multiple shells:
HNM shell ALLASHELL drops Absolute Virtue. For the next week anyone in that shell would get +10 HP, +10 MP, and +1 STR. A member of WELIKEPIE kills Leaping Lizzy allowing for a +1 HP bonus. If you now had both shells active you'd have +10 HP, +10 MP, and +1 STR since similar buffs don't stack. Another member of WELIKEPIE kills Jaggedy-Eared Jack and earns a shellwide +1 DEX buff. Now you're at +10 HP +10 MP +1 STR +1 DEX. You join PIKKOFANCLUB and activate the pearl to discover a +15 MP +1 AGI buff from killing Charybdis. Now you're at +10 HP +15 MP +1 STR +1 DEX +1 AGI. A new member joins ALLASHELL and needs to get his sky earring and after victory the shell (along with the shells of a few PUG members) earn a +20 dark resist buff. ... etc ....
This kind of system would allow for lower level and repeatable content that is currently non-rewarding to give bonuses to the shell as a whole incentivizing inclusion of more people. Having a few lowbies in an HNM shell is currently an absurd concept, but if they're doing lower level things that would buff the HNM shell to assist in higher level content they would be valuable. It would also incentivize people to do a broader variety of events and join a larger number of shells (strengthening serverwide social cohesion) to increase their overall strength. The thing to balance is the power of having these bonuses as opposed to the increased social cohesion on the server that they could bring, though you'd be hard pressed to contend that getting people together as a community could do anything other than strengthen the community as a whole. Maybe the smaller buffs would only last a day while some major accomplishment buffs would last a week. Maybe certain special accomplishment buffs would last only a matter of hours but would be very strong (i.e. Nefarian/Onyxia kill buff in WoW). The applications are endless. Maybe some buffs could even flag the shell to get "shell leves" that give access to HNM style leves ... so if you drop Fafnir you might get periodic access to a leve that allows your shell the ability to summon Nidhogg. Stuff like that.
Anyway, these are just some ideas I've had rolling around in my head for years. I've often visualized how hierarchical shells could have improved FFXI. The best example would be a THEOFFICERSCLUB shell on a server where HNM GMs and officers could hang out to hash out differences, talk strategy, and gloat about victories ... the drama and peacekeeping it could simultaneously bring would be glorious to behold.