I am being encouraged/offered to join all of the guilds (fighter, thief, and mage)--and also being told to join the Imperial Guard.

Is there a disadvantage in joining multiple guilds--am I going to ruin my chances later in the game?

Some guilds conflict with each other.
The one I am aware of is, unless you do something clever your going to have a conflict between the Fighters guild, and the Thieves guild.

It shouldn't have an effect on the main plot of the game.

Fighters Guild and Thieves Guild do conflict, but it can be worked out. I was both Mastermind of TG and -something- of the FG.

It gets sorted out eventually. Just talk to people in guilds and employ some common sense.

joining multiple guilds at one time is hard though, you can't keep track of all your quests and such

the easiest is to join both fighter and thief guild at the same time. after that you can join one guild at a time.

Join one guild at a time, with the only exception of fighter and thieves. Otherwise you will never be able to kep track of all the quests they give you, not even with the new indexed journal feature

also, apart from fighter and thief guild. you might as well take one quest at a time on other guild. thus you don't get overwhelmed by too much quest.

This advice may seem a bit boring, but that's because i find the game more enjoyable at lower levels. Join only one or two guilds per character. Each has enough quests and reward items to see you modestly powerful and there's plenty of miscellaneous quests to kill time in between (and make you godlike, if that's what you want). The guild quests also seem to be geared towards low level characters. It's just no fun being the Nerevarine, Hortator, Archmage, Archmagister and Guardian and then being sent out on a quest that any level 1 drop kick could complete. In fact, it's mildly insulting. I think you'll enjoy the guilds a whole lot more if you create a new character each time.

It's also less than convincing (in terms of roleplaying) that a character straight off the boat can become the kingpin of every major faction (and therefore the most powerful person by far in all Vvardenfell) in less than a year of game time. But that's just me.