Here is to be collected links to the most instructive posts on how to modify the Fostex T50RP, mostly from this thread: Just listened to some Fostex T50RPs today... WOW!
This is not for "Thunderpants" - only modifications keeping the standard cups
BMF is bluemonkeyflyer's mods.
BMF's Fostex T50RP Incremental Mods and Measurements (FIMM): FR and CSD/Waterfall Graphs for Different Configurations Including DBV #3 Includes:
1. DBV #1, DBV #2 ("Dmitry's Mod"), and DBV #3 ---> DBV #3 is recommended 
2. Tutorial and Pictorial for "Simplified and Consolidated Tutorial and Pictorial for DBV #3"
3. DBV #3 Variations with Grodan Rock Wool Mod, "Naked Driver" Mod, and Rite Aid "First Aid" Cotton Balls Mod
4. Tuning Rules of Thumb for tweaking your "Initial Build" to best meet your preferred sound qualities and "audio chain"
5. "How To" make, implement, and test Modified Bass Ports (Temporary External and Permanent Internal versions) and Modified Baffle Ports
6. Repairing Stripped Cup Threads and Hanger Holder Threads
7. Pad Rolling Measurements for 8 Pads using an All Stock T20RP mk2
8. Hundreds of Incremental Mods and Measurements "How To" Pictures and measurement graphs (FR, Waterfall, Spectrogram)
9. Preparing Rite Aid "Absorbent Rolled Cotton" and J&M Fiberglass
10. Using templates and a digital scale for balanced Left and Right Channels
11. Comparison pictures and "All Stock" measurement graphs of T50RP, T40RP mk2, and T20RP mk2
12. Comparison measurement graphs with Panasonic WM-61A mics mounted on Etymotic Triflange Ear Tips vs Etymotic Foam Ear Tips
13. Comparison measurement graphs of my LCD2 v.1 headphones
14. Recommended installation of Dynamat on the ear side of the drivers
BMF 8.1
This link includes:
1. V8.1 Mod Tutorial Text (Outdated - Use DBV #3, above)
2. V8.1 Slide Show (Outdated - Use DBV #3, above)
3. Room Equalization Wizard (REW) Setup Summary
4. Links to BMFs Incremental Mods and Measurements - REW .mdat files - Useful for learning how to use REW
5. Phantom Power Supply & Panasonic WM-61A Mic Slide Show - "How To" Build Your Own Measurement Kit
6. A Relatively Simple Mod Variation (Outdated - Use DBV #3, above)
All the following mods are Outdated:
BMF 6.3
BMF 6.1 vs 6.2
BMF 6.2
BMF Transpore mod
bluemonkeyflyer's modified rastapants with picture walk through
more from bluemonkeyflyer (applying dynamat)
bluemonkeyflyer on temporary closing the cups in between mods:
bluemonkeyflyer compares unmodded and modded T50RP to LCD-2 etc.
follow up
simple mod
RASTAPANTS: Rastapants 2 by mrspeakers:
Rastapants 2 840 Pad Edition:
Rastapants 1 by mrspeakers
Rastapants by mrspeakers pictures
mr speakers measurements
mr.speakers sbour RP2 and O2 pads
HDman T50ResPonse
Arleus on modification and measurement - Spectrograms and SPLs
mmda - simple glue and clay mod
BmWr75 simple mods (a BMF variant)
LFF "Paradox"
It is a secret.. elaborated here
Magick Man's "Smooth Operators"
hans030390's modded T50RP (Updated 12-15-2011)
Fat person T50RP by snakeeater69
Very very easy mod with K240 Sextett pads by RexAeterna
mmayer167 easy mod with O2 pads
rawster picture walk through RP2
SPwild's mod
Cheap mod by dogears
Jonclarke doing tidy work with Paxmate and Dynamat - pics
PhaedraCorruption picture tutorial
ambchang's two mods comparison
Faust mod:
b0wl1ngs variant:
SlaRe comments: "Tried this one, seems like the best best if you don't have paxmate. It's impressive what just a thin piece of felt glued over the driver can do, really good isolation too."
Smeggy's old setup:
Rastapants in the flesh:
SlaRe comments: "Works best with 840 or O2 pads apparently. The leeperry mod is basically the same thing, only you leave the white felt over the driver."
LFF headband suspension
Twinster's sound reflection cardboard cookie
Pwnm30rdi3's Cup Re-paint Tutorial:
joelpearce's Rock Wool Mod for "Naked" Drivers:
How to open and re-assemble while trying out different mods; How to remove and re-assemble the headband hanger
Scroll down to "How to Open and Re-Assemble Fostex T50RP Headphones[size=11.818181991577148px]"[/size]
AnotherN00b sum's up modding
Fostex T50RP Modification:  A Summary of Methods, Materials, and Their Possible Effects (Out Dated - No Longer Supported --> Go to: BMF's Fostex T50RP Incremental Mods and Measurements (FIMM) at the top of this page)
Armageis on damping
High End Phones-Comparison
Exploded parts view
Tyll Hertsens explains about orthos in general and why they are especially sensitive to good acoustic damping
Making and using a sound testing kit with mics, phantom power box, and Room Equilization Wizard
A basic modding demonstration and explanation for those wanting visual guides.
Megathread search tool by ludoo
Beware that pads have influence on sound, and the mods are adjusted to the pads. Always keep in mind what pads are used by a modder.  
Shure HPAEC840 Replacement Ear Cushions For SRH840 Headphones
Shure HPAEC940 Replacement Velour Ear Cushions for SRH940
Beyerdynamics DT990 Velour pads (black or grey)
Fischer FA-003 pads
Audez'e LCD-2 pads
Stax 007 pads
Smeggy's description of various pads
Useful "Sock Mod"
to avoid those platic earpads making you sweat. I did this - and ignored the cardboard part, just stuffed the cloth under the pads :)
HD280 pad mod by satwilson 
Self-adhesive spare parts pad mod by ardilla
LFF headband mod
micmacmo's leather suspension headband, inspired by LFF's headband mod
Total makeover mods (new cups)