You can join only one of the 3 houses (Hlaalu, Redoran and the mages one) but you can apply to any other guild.
Check
http://www.morrowindchronicles.com/l...ionsguilds.htm for details on reaction bonus/malus between guilds and houses.
Your actions will have a lot to do with how you are percieved, so don't join two enemy guilds.