As of Roster 2.0.0, this is all possible
In a nutshell, the current roster is not designed to handle multi-server, multi-guild, a collection of random characters, or multi-allegiance/faction (horde AND alliance) setups.
With a bit of custom editing you may kludge something workable but you're kinda on your own there (well, excepting public help but the devs won't be stepping in helping unless they're in the mood) and the posts that have been made to modify some of the SQL queries and include the GuildID parameter do not work on all pages so it is only a partial solution.
It's an issue we're aware of and something we're looking at trying to accommodate but it's not high on our priorities as there are many other more important features we're currently implementing or improving (eg. improved language localization, pet info, reputation info, guildbank, etc.).
Another roadblock on this issue is that despite countless requests for the people that want this functionality to provide us a full specification of all the possible combinations we would have to cater for and what is actually possible (eg. different faction/same server/different guild name, different faction/different server/same guild name, etc.) we have had absolutely NO responses. If people are only willing to ask, but not provide feedback when we ask for it, then the chances of this feature moving any higher up the priority list are pretty slim.
At this stage, for the sake of simplicity, we recommend having a separate roster directory on the webserver and database for each guild.
Original Post By: AnthonyB