Far from complete, but its a start. 

-> Debugging / Reverse Engineering / Assembly.
[OpenRCE.] Its a good place to start. Gogogo!
[http://directory.fsf.org/devel/debug/] FSF Debugging Tools (heap corruption checkers etc...)
[gdbinit.txt.]A Handy GDB config. Save as .gdbinit
[gdb_tips.txt.]A Handy GDB tut to get you going.
[Beginners Guide to Basic Linux Anti Anti Debugging Techniques.] CodeBreakers Journal. I'll look it over if I can keep my  hands off of my Xbox360.
[ IDA Pro: Disassembler and Debugger.] The only game in town.
[Mammon_'s Tales to his Grandson..] Registers, Memory, and how Assembly Language came to Mankind.
[x86_64 Instruction Reference.] Don't click unless you know what Relative stack addressing and what 'storq' 'jge 0x00000ff $edx' is.
[x86 Instruction Reference.] Same as above, just without the extra registers, quadwords and headaches.
[How to Write Your Own Packer.] by Big Boote for CodeBreakers Journal. Writing packers, you know you want to.
[64-Bit - Programming and Assembly Issues.] by Thorsten Schneider. Painful & necessary, this may help.
[Award BIOS Reverse Engineering.] by Darmawan Mappatutu Salihun.  Hey, Why the hell not!?.

->Sploits!
[bypassing-dep.pdf] Bypassing Windows Hardware-enforced Data Execution Prevention by Skape
[defeating-w2k3-stack-protection.pdf] Defeating the Stack Based Buffer Overflow Mechanism of Windows 2003 Server by David Litchfield
[Smashing the stack for fun and profit]A classic. by Aleph1
["Buffer Overflows Complete" By detach at hackaholic.org.] If I were to explain buffer overflows to someone, it'd go something like this, a must read. *Ahem* Dblitz, looking at 
you.


-> Executable File Formats
[ELF.pdf] Executable and Linkable Format (ELF)
[p61-0x08_The_Cerberus_ELF_interface.txt] The Cerberus ELF interface by mayhem
[pecoff.doc] Microsoft Portable Executable and Common Object File Format Specification
[www.elis.ugent.be/diablo] Diablo: a retargetable link-time binary rewriting framework
[Overview of PE file format.]
[PE Format.] Windows IT library DOT com
[Wotsit.org.] This site contains information on hundreds of different file types, data types, hardware interface details and all sorts of other useful programming information; algorithms, source code, specifications, etc.
[Portable Executable File Format - A Reverse Engineer's View.] by Goppit for CodeBreakers Journal.

-> Fuzzing
[lcamtuf.coredump.cx/nictuniema.txt] Superpositions and Successive Approximations in Exhaustive Vulnerability Testing by Michal Zalewski
[fuzzing_concepts.pdf] Fuzzing: Breaking software in an automated fashion (concepts) by Ilja van Sprundel
[TAOF: The art of fuzzing.] Some kinda fuzzer thingamabob.
[The Evolving Art of Fuzzing.] by Jared DeMott. He also wrote GPF. 
[Wfuzz ] 
[ Net-Force Tools (NF-Tools, Firefox Add-on) ] 
[ XSSScan ] 
[ Web Hack Control Center (WHCC). I like the name] 
[ screamingCobra ] 

-> MacOS X
[MachORuntime.pdf]
[mach-o_infection.ppt]


-> The InterWebs
[W3AF:Web Application Attack and Audit Framework.] I've tried it, I like it.
[XSS (Cross Site Scripting) Cheat Sheet.] Just so damn handy.
[web_lookuptable] Lookups for html codes and such.

-> Misc
[Rob Slade's Security Bookshelf.]
[Penetration testing.] A blog/site/thing devoted to one of my fave past-times. I thought it was campy, but gets got some good links.
[Security Readiness Review Evaluation Scripts.] Straight from DISA.MIL. Having looked over some of the checklists, and run some of the Eval scripts, I can say they are well thought out and will boost system security
200%. It'd be nice if the DOD actually put them into practice, then maybe some large Asian nations wouldn't stomp all over their systems. Anycase, test out your box if you'd like a few shortcuts to hardening. *shrug*
[Webster's New World Hacker Dictionary.] Just as it says. 

-- P.S: Thanks to http://powerhacker.net/codebreakers.html for some of the prime content, and general layout.