Languages

Native Language: It's a sign of respect if you speak to someone in their native tongue. If you and a creature share a language (like common) but you speak to them in their native language (halfling, dwarven, etc), you get a +2 circumstance bonus on any social roll (bluff / diplomacy / intimidate). This does not apply if the only language you have in common is that one language. In group settings, this might alienate people without that language, giving -2 to any social rolls against them if you're regularly speaking to someone else in a language they can't understand. Using tongues or similar magic to emulate a language (or telepathy or truespeech) does not provide any bonuses or penalties. 

Existing Language Modifications

Draconic: Generally considered to be the language of arcane spellcasting as well as draconic creatures. While speaking in draconic, you have a +2 circumstance bonus to any ability that allows you to conceal spellcasting as normal speech. This bonus does not apply if you just randomly speak in draconic to cast a spell, the conversation must already happening in draconic. (If a bunch of people are talking in common, it's more suspicious if you start talking in draconic all of the sudden). 

Infernal: The language of infernal is very specific and legalistic, with each word implying not just one thing, but also specifics about that thing. Where as in English "kid" can refer to a young goat or a young child, infernal has no words with duplicate meanings. As such, infernal gives the following benefits: 

Contracts written in infernal have minimal loopholes (or none). Wordplay will not allow you to weasel out of an infernal contract.

Wishes made using infernal are less likely to be misinterpreted by a literal genie. A jerkass genie might still find ways to screw with you. 

Communications in infernal require 50% more words than in common. This affects things like sending or magic mouth or other spells where the number of words is relevant. 

Abyssal: The chaotic language of Abyssal is the opposite of infernal. Different words can have five or ten different meanings depending on context. As such, abyssal carries the following traits:

Contracts are typically not written in abyssal as it would have to be several pages per clause, and most demons don't honor contracts anyway.

Wishes made in abyssal are ridiculously easy to misinterpret, especially if the wish granter wants to purposefully mess up a wish.

Communications require 50% less words- spells like sending or magic mouth can have more words, but there is a 20% chance that a character without context could misinterpret the meaning of a shortened sending or magic mouth. (You get a sending, it means either: There is an army of people headed towards Lancaster, or Lancaster will soon drown in torrential rain, or I am happy to be where I am and not in Lancaster.)

This is also true of the Protean language. 

Treant: The language of the trees is slow and specific. Each one word has twenty or more syllables and takes a full round to say- however each one word contains as much information as a full sentence. As such, sending spells, magic mouth spells, and other magical communciations in treant can transmit a number of sentences rather than a number of words, drastically increasing the amount of information that can be sent. However, the casting time for such spells is doubled, and it takes 1 round per sentence for the information to be received. 

Code Languages

Codes: Codes can be taken in place of languages. A code is a method of communicating with someone who shares a language with you. They must also have taken the code as a language.(So they require to languages, a shared language (typically common) and the code.  This can allow unusual communication styles that enemies would have a hard time overhearing. As codes, they do not get deciphered by Comprehend Languages or Tongues, though they can be deciphered with Linguistics. Keep in mind Bluff can be used to transmit a secret message to people as well if this is a one-off. 

Linguistics can be used to create coded messages (especially written ones). Having a cypher to decode the languages can allow them to be made and sent without checks. 

Morse Code(code): This would allow a series of beeps or taps to communicate with each other. Communication is not as simple as a language, and it takes a move action to communicate with this. 

Sign Language (code): Drow sign is a secret language, but sign language can be taken as a second language. It requires a base language that is shared (Common Sign is thus the easiest). This allows quiet conversation. If you don't want a shared language, the Bonded Mind teamwork feat is used for a generic quiet communication method. This is considered a code. Spells like silent image could transmit sign language. 

Music (code): By taking the Music language, you can communicate with each other using various tones. (Like a pre-determined code). This might make for long distance secret communications. This is a code, not a language. It requires a shared language between both people with this language. A perform skill could be used in place of Linguistics to decipher this. A bard can submit information this way during one of his bard performances (but not while using a bard masterpiece or while using perform to cast spells- as the music used is predetermined by the masterpiece or perform check. 

In times of stress, a Perform check (DC 15+ based on amount of stimuli) might be needed to transmit a message. Spells like Ghost Sound could transmit a musical message. Spells that cause instruments to play themselves could transmit such a message, though spells that the caster doesn't retain control of might send the same message over and over. Sheet music could be a written form of this code. 

Touch-Tap (code): People communicate by tapping each other. This can be done while next to each other, or with telekinesis or mage hand. This communication is silent, and it takes a standard action to communicate like this. A touch spell can be delivered while talking to someone in this manner. Creatures with tremorsense could receive communication at a distance by tapping the ground or a web or something. Creatures with blindsight (not blindsense) could use signals to communicate this way while within range. 

Emotion Code (code): Creatures with an empathic link (like mages and familiars) who can detect each others emotions, can create a morse-code style communication between each other as a language. Mages with familiars can take the language themselves (the familiar need not also take the language), but any other 2 characters must take it together. This involves specifically attempting to send emotional readings over the link in such a way to be decoded by the receiver. This allows extremely complex ideas to come across, similar to telepathy. Redundancies are used in case of mistaken signals (as true emotions can cloud the ability). This cannot be used when under the effects of any emotional ability (such as fear or calm emotions or rage). In times of combat or stress the sender must make a bluff check DC 20 or more (decided by Gm based on level of stimulus) to properly send the message without it being disrupted by real emotions. 

Light Speak (code): This allows complex ideas to be shared with various lights. With flashing lights, conside Morse Code instead, but this would allow complex codes based on colored lights (such as with Dancing Lights) or with silent images (need not be colored light, could be pictograms or something). In this case, communicating uses the same action as controlling the spell effect. 

Thief's Cant (code): This uses regular words in new ways to convert new messages. Two people with this will never misunderstand each other when using bluff to convey a secret message, and listeners have a +5 penalty to their Sense Motive DCs to understand the message. This is a common code amongst rogues. It being so common makes it more likely other people will understand you (it's a commonly taken code language) but also it's slightly more likely the wrong person will know what you mean. (Because it's so common). 

Read Lips: This allows a deaf character or characters in silence to understand anyone speaking in any language they know without the need of perception checks. Someone trying to conceal their mouth (like using ventriloquism) or in dim lights or at a distance further than 10' away would require perception checks as determined by the DM.

Braille Writing(code): This allows people to write using bumps. This can allow written messages to be read in darkness, or by blind people. Scrolls written in this way can be used in darkness or by the blind.