Chameleon Circuit is a british band who sing songs about Doctor Who. I've recently bought their first two albums but I'm struggling to pull apart the lyrics and figure out which if any episodes and characters they're referencing.
For starters: the band name Chameleon Circuit is named for the part of the TARDIS that is responsible for changing its shape when it lands.
As for the songs, here's the entire list, with more details on the ones you already had as well:
An Awful Lot of Running - Aside from being a general comment on the amount of running in the show, multiple characters have made this comment, including some companions. The lyrics themselves start out as a general description of what it's like for a companion when they first meet The Doctor but they end up being a clear reference to Donna Noble at the end of her run, as DoctorDonna.
Gallifreyan History 101 - This is a summary of what we knew about Gallifrey from the old series; I suspect it's a partly sarcastic commentary on the fact that RTD got rid of Gallifrey, based on the lyric "I just hope it doesn’t get messed up by Russell T Davies"
Count the Shadows - This is a nice plot summary of the episode Silence in the Library
Shipwrecked - Not sure about this one; it appears to be about The Doctor stranded on a dead TARDIS with no Time Lords left to rescue him but I'm not sure what the last verse about the "green glimmer of hope" is referring to, possibly The Rise of the Cybermen episode.
Type 40 - This is basically a summary of the Tenth Doctor's run from the point of view of the TARDIS herself. References include "huon energy" from Runaway Bride, the Titanic, the 6 people in Journey's End piloting the TARDIS, plus some references from the old series about TARDISes.
Blink - Easy one; a plot summary of Blink from the POV of Kathy, Sally's friend, because one of the first lines says 'I sent you a letter, to make you feel better, 'bout the fact I was gone.' Kathy wrote Sally a letter from the time she was sent back too.
Exterminate, Regenerate - This appears to be a lyrical interpretation of Davros's speech to Ten in Journey's End. This song actually can be perceived from each side, either Davros speaking to the Doctor or the Doctor speaking to Davros.
K9’s Lament - This is basically K9's response to being left behind with SJS instead of The Doctor keeping him as a companion.
Journey’s End - Basic plot summary of Stolen Earth and Journey's End
Friends of the Ood [Acoustic] - An "ode" to The Doctor from the Ood he freed in Planet of the Ood.
The Subwave Signal - No lyrics, but this is a reference to Harriet Jones' subwave network that is used to call The Doctor in Stolen Earth.
Regenerate Me - Nothing specific, just a general reference to The Doctor being able to regenerate.
Nightmares - This appears to be sung from The Doctor's perspective, but it's also about The End of Time; leading up to this episode Ten had begun to see himself as "out of control" and heading for personal catastrophe, in addition to the disaster that arrived in that episode.
Travelling Man - Seems to be just a general song about The Doctor saving the day; it does make reference to the Sarah Jane Smith episode where Eleven claims he can regenerate 506 times.
Everything Is Ending - This is a lyrical version of the scene at the end of Flesh and Stone between Amy and Eleven; she had just nearly been killed by the angels, and is coping by coming on to the Doctor; he is just realizing what the cracks mean and that time is collapsing.
Mr Pond - Basically this is Rory taking the Doctor to task for a number of things, including his interference with Amy's life, her infatuation with him, and how dangerous he is to those around time.
Kiss the Girl - Craig Owens from The Lodger singing about his girlfriend, when The Doctor asks about her.
Knock Four Times - The lyrics are almost word for word what Carmen tells The Doctor in Planet of the Dead, though out of order.
Teenage Rebel - Another general description of The Doctor, who ran away from home when he was ~200, or roughly the equivalent of a teenager in human years.
Big Bang Two - A basic plot summary of the very end of The Pandorica Opens and all of The Big Bang
Eleven - No lyrics, but clearly a song about The Eleventh Doctor. It's a re-arrangement of Eleven's leitmotif (called "Next Stop Everything" but most often identified with the track "I Am The Doctor").
The Sound of Drums - Events of Last of the Time Lords from the Master's perspective
Silence and the End of All Things - This is a lyrical interpretation of Eleven's speech to little sleeping Amelia near the end of The Big Bang just before he is "erased".
The Doctor is Dying - A plot summary of The End of Time, Ten's last episode before he regenerated; "I don't want to go" are Ten's last words, as he's regenerating, and Ood Sigma tells him he will "sing him to sleep".
Still Not Ginger - This is a collection of things Eleven says in The Eleventh Hour soon after regenerating. Note that the title of the album, Still Got Legs, is from this song.
"Shipwrecked" refers to the episode "Rise of the Cybermen". They are singing about what the Doctor is thinking when the Tardis crash lands in the parallel universe, and the Tardis is supposedly dead. There is a clear reference at the end of the song when he says, "try to keep them safe, they don't know what lies out there" - Rose and Mickey don't know what could possibly be outside of the Tardis in a world that looks like their own but is different.
Shipwrecked is clearly about Rise of The Cybermen. In the song it says “green glimmer of hope” referencing the bit of the TARDIS still alive and “If I use some of my life we’ll use it so escape this place” referencing that the doctor uses some of his regeneration energy to repair the TARDIS.
I thought regenerate me was the master singing about how the doctor can't defeat him and such, and exterminate regenerate was: The first verse was davros, and the second was the doctor. And for blink I don't think it's from the doctor's perspective i think it's from Sally's friend that got zapped back in time at the beginning of the episode