A perception filter is a telepathic effect caused by Gallifreyan technology often associated with a TARDIS and various related objects such as TARDIS keys, which shifts perception away from the object the filter is cast on. As Martha Jones put it, "you know it's there, but you don't want to know it's there". (DW: The Sound of Drums)
It is a possible explanation of why the blue box that is the Doctor's TARDIS fails to be noticed when parked in unfamiliar territories across the time and space. Time Lords can use their TARDISes to place perception filters upon small objects such as Chameleon Arch fob watches in order to keep them safe. (DW: Human Nature)
Particularly intelligent people are immune to the effects of a perception filter (DW: Human Nature) much like psychic paper (DW: The Shakespeare Code). It also does not work on Time Lords (DW: The Sound of Drums). Once one becomes aware of a perception filter or has their attention spiked, it ceases to work. (DW: Utopia, TW: Everything Changes)
In Cardiff, the Doctor's TARDIS, in conjunction with the Cardiff rift, accidentally applied a perception filter to a slab of pavement on Roald Dahl Plass by transferring its dimensionally transcendental properties (DW: Boom Town). The Torchwood Institute made use of this by having Torchwood 3 convert that tile into an entry their base, referred to as the "invisible lift". (TW: Everything Changes)
In The Year That Never Was, Martha managed to shield herself from detection using her TARDIS key which the Doctor had equiped with one of these filters. It prevented her from being detected and allowed her to set up a plan to defeat the Master. (DW: Last of the Time Lords)
The Doctor Who Confidential accompaniment for Human Nature suggests that Timothy Latimer, the boy who was immune to the perception filter, was a genetic mutant born with an extra piece in his brain. The final script makes no mention of this, although the Doctor does note that he has an extra telepathic synapse in his brain, accounting for his strange abilities.
The series has yet to establish when the perception filter was installed or activated in the TARDIS for the first time. It would appear to be a relatively recent innovation (possibly Time War-related?), as there are many occasions in the original series and 1996 telefilm where no perception filter effect is in evidence.