The GM can limit a typical familiar's ability to aid another on skill checks
On Skills on Aid Another says
You can help someone achieve success on a skill check by making the same kind of skill check in a cooperative effort. If you roll a 10 or higher on your check, the character you're helping gets a +2 bonus on his or her check. (You can't take 10 on a skill check to aid another.) In many cases, a character's help won't be beneficial, or only a limited number of characters can help at once.
In cases where the skill restricts who can achieve certain results, such as trying to open a lock using Disable Device, you can't aid another to grant a bonus to a task that your character couldn't achieve alone. The GM might impose further restrictions to aiding another on a case-by-case basis as well.
(Emphasis mine.) This means that the GM may rule that, for example, the typical less-than-level-4 master's familiar—that usually can't speak and that usually can only communicate empathically with its master—may be unable to aid another on Knowledge skill checks and other skill checks where what it knows could be useful… if only it could only speak. (A more generous GM could allow the familiar to communicate that the master was getting warmer or getting colder so as to still grant the aid another bonus on some skill checks, although this bonus may take a while to be realized!)
Also, the GM can arbitrarily limit the number of creatures that can aid another on a skill check.1
Further, other restrictions may apply: On Familiars on Familiar Basics on Skills says, "Regardless of a familiar’s total skill modifiers, some skills may remain beyond the familiar’s ability to use." In other words, the GM is allowed to just say to No not only to a master's familiar's attempts to aid another but also to the familiar's ability to use a skill at all.2
Finally—and obviously—, there's no way a familiar whose master and familiar both lack ranks in a trained-only skill can aid someone with a trained only skill. If neither master nor familiar has ranks in the skill Disable Device, for instance, the familiar just can't aid anybody on Disable Device skill checks.
However, despite the possible restrictions that a GM could layer on a familiar's use of skills—therefore on aid another attempts—, this GM and the GMs with which this player has gamed have all been extremely liberal with what a familiar can accomplish. Having a familiar make aid another attempts to assist with skill checks has always been one of the reasons to have a familiar, especially at low levels.
In addition, while a +2 bonus on many skill checks at first blush may seem extremely powerful, by the time the master's relatively competent (say, level 5 or so?) that +2 will often be forgotten—or even go unused—because the master can already make all the checks he needs to make on his own.
On Combat on Aid Another says
In melee combat, you can help a friend attack or defend by distracting or interfering with an opponent. If you’re in position to make a melee attack on an opponent that is engaging a friend in melee combat, you can attempt to aid your friend as a standard action. You make an attack roll against AC 10. If you succeed, your friend gains either a +2 bonus on his next attack roll against that opponent or a +2 bonus to AC against that opponent’s next attack (your choice), as long as that attack comes before the beginning of your next turn.…
(Emphasis mine.) Because the typical familiar has a reach of 0 ft. because of its Tiny or littler size, the typical familiar doesn't threaten an area, so it's only very rarely in a position "to make a melee attack on an opponent that is engaging a friend in melee combat." (Even arming a familiar that can wield one with a reach weapon—like kitting out Mr. Nilsson with a lance—is typically no help here!)
A bigger familiar is more useful in this regard, of course, but with a bigger familiar comes new problems. (Like the fact that the bigger familiar still only has half its master's hp, yet it's being ordered to enter melee!)
1 The System Reference Document for D&D 3.5—on which Pathfinder is based—omits most of that earlier game's examples, including the one from its Player's Handbook of only one creature being able to aid another on a Heal skill check made to stabilize an ally "because a third person would just get in the way" (66). As an aside, this reader recommends not allowing 3.5 example writers to perform your surgery.
2 In another omitted Player's Handbook example, this statement specifically mentions as an example the skill Craft as a skill a familiar is incapable of using (52).