First step is to identify what kind of secret identity you need, and what kind of disguises do not simply work.
For example, if your role in the secret organization is to make connections - then you cannot form a working secret identity by wearing a mask 24/7. Full face covers must be removed when entering certain locations. And I cannot stress enough how suspicious or awkward those 'masks' appear. The moment you see someone trying to keep their face entirely hidden, you know that they are either hiding something or up to no good. Not to mention the number of players who wear those 'hooded masks' to appear 'cool' - so most of us are entirely accustomed to ignore these 'hooded masks' as proper form of disguise. Just when was the last time you saw someone asking 'Who are you?' from a masked character?
So in this very public role, a best secret identity could be entirely public persona who dons a mask when he deals with his or her secret backround organization. After all, the idea behind a mask is to protect your identity when you need to have your identity protected.
So what makes a disguise that works better?
Statistically speaking, some of the head models are far more commonly used than others. It is one of the reasons why I often link this song on this forums. Therefore, your character's hair style and colour are much more important when someone tries to identify your character. After all, almost all of us play this game from the isometric game view of the Exploration camera mode.
In stock NWN2, it is impossible to change your character's hairstyle and colour without using some kind of editor to modify the character .bic. Luckily though, next to Maltz' Store in Baldur's Gate we have a Barber Shop where you can purchase wigs, new hair colours and styles for 100~ gp a piece.
A single wig is not enough. You must also come up with unique appearances to all of your secret identities. Picking a colour scheme is a good idea. For example, Bob as a member of the clergy of Ilmater could be wearing nice light shade of browns - while in his true profession of a Master Cat Burglar he dons glaring pink outfit. Yet picking colour schemes is not all you can do. Mechanically speaking; Padded Armour, Chain Shirt, Breast Plate, and Full-Plate are the best armours to have. But the fact remains that we also have Leather Armour, Studded Leather Armour, Hide Armour, Chainmail, Scale Mail, Banded Mail, Splint-Mail and Half-Plate. These armours while mechanically weaker have their own unique appearances and are often really affordable to purchase. For example, I recently purchased a +4 Hide Armour for 2 000 gp. Not to mention that if you gain your Armour Enchantment bonus from bracers, it does not really matter what armour you have. So think carefully what kind of situations you can expect to end up in while in your disguise. If Bob the Holy is usually seen wearing a shiny full-plate, he does look very different if he is suddenly wearing a blue padded armour with a ginger wig to cover his bald head. Additionally, it does help to have new boots and cloaks to go with your disguise as well.
Because we can right click other characters to examine them, it is also a good idea to use our server's custom 'bio' tool to store three distinct 'biographies' that detail each of the disguises individually. It is a good idea to use fake ears, noses, and facial hair with all your 'disguises.' This way you can make the three possible disguises as distinct as possible.
It is also very important that your character's "name" is not a name your character uses for anything. For example, Xres'hir Droi'brather, could assume the aliases; Bob Stronghill, Jack Evenmedows, and Alexander Decander. This way, if anyone accidentally calls you "Xres" - it is very easy to point out the error. But as for situations where someone Bob, Jack, or Alex when you are not in the different guise, you could try to play it off as if that person had just introduced themselves or someone who has just joined the discussion. "Alexander? Why, it is a pleasure to meet you. My name is Jack Evenmedows."
You should not underestimate the need to invest in all social skills; Appraise, Bluff, Diplomacy, Intimidate, Taunt, Perform, Sense Motive, and Lore. This allows you to give your disguises abilities the other disguises do not have. For example Alexander could be highly diplomatic. Jack someone who relies on intimidation, and Bob a sly tongued merchant baron.
And finally, there is the last thing you have to do for a good disguise. All your disguises should have their own distinct mannerism and speech patterns.
- Bob: Hello, it is a nice day today.
Jack: Hullo, this a nice day.
Alex: Helloz, it iz a nize day todayz.
And you should not forget about the importance of emotes. Emotes allows you to highlight their different gestures. Bob could be weasely in his behaviour. Jack like lumbering giant, and Alex could have a very noticiable limp.
Now, if you set out to everything I've listed, will this mean you will not be metagamed or discovered? Well, the unfortunate thing is that you can still be metagamed, you can still be discovered, but I do not see what else you could do to have a good disguise. And even if you get cought due to metagaming, this sheer amount of effort you have seen could be used combat metagaming, perhaps giving your character a chance to flee and perhaps even complete what he was set out to do.
People do often complain about how you can see floating name tags if you hover your mouse cursor above a character. Personally, I am having troubles remembering that such a 'feature' even exists in this game. No one is forcing you to move your mouse cursor on other characters, most of the time you do not even have to if you are not going to attack them. So the issue of floating name tags lies solely on you yourself.