Kentie's Launcher is a replacement for DeusEx.exe, and will help to manage your mods. Not strictly necessary, but it makes it a lot easier. Kentie also has a Direct3D10 rendering engine.
Core Deus Ex Mods (Bug Fixes Only)
(NOTE: Both types of Core Deus Ex Mods modify the same files, DeusEx.u and DeusEx.int; therefore, you can only use one at a time.)
Deus Ex v2.0 is a community-supported ongoing patch effort, with no extra content and minimal/no changes to the gameplay rules.
Deus Ex: Human Renovation, by G-Flex, is an offshoot of Deus Ex v2.0.
Core Deus Ex Mods (With New Content)
Shifter adds a lot to the basic Deus Ex experience. Some rebalanced weapon stats, bug fixes, restored content, unique weapons, updated augmentations, new augmentations, and so on.
(NOTE: Shifter includes a new skill point system which gives you points for kills and for stealth. This is pretty problematic for the balance of the game because of the sheer number of extra skill points you can get by min/maxing. It also tends to slant tactics in favor of killing everyone, because getting the killing bonuses is a lot easier than getting the stealth bonuses. Therefore, your first playthrough should either be with vanilla DX, or with a Shifter derivative that does not have the skill point bonus system. (BioMod fits that bill.) )
Deus Ex Enhanced is based on Shifter, and provides various additional fixes and upgrades. (There is a Direct3D 9/OpenGL compatible version, kinda buried on the mod's page. Just noticed it.)
BioMod is another derivative of Shifter, including most of its' fixes, but with significant changes to how the augmentations work.
(WARNING: BioMod changes the Swimming skill to a more general Athletics skill, and decreases your base jump height to make it worth investing points into; according to DarkRealityX/DXNathan from GameFAQs, this can cause you to become stuck during the last segment of Mission 2 if you are taking the rooftop approach, because you may not be able to jump up to some ledges.)
hejhujka's DX Hardcore helps make Deus Ex fresh again by changing the difficulties into different styles of playing.
Unified Deus Ex merges Shifter, BioMod, and Deus Ex Enhanced into a single package. This package also adds the ability to toggle certain functions (such as the Shifter skill point bonuses) off and on with flags in DeusEx.ini. The current version also includes upscaled UI elements; there will be a version without in the future.
To go along with the Core Deus Ex Mods, Emualynk's mod installation guide is a good read. http://www.gog.com/en/forum/deus_ex_series/deus_ex_augmentation_guide
Deus Ex: New Vision, which recently came out of beta, updates Deus Ex's world textures, resulting in a much nicer-looking game. Also includes Kentie's launcher, Kentie's updated rendering engine for Direct3D 10, Chris Dohnal's updated rendering engine for OpenGL, and an alternate updated launcher by Hanfling.
Project HDTP, for High-Definition Texture Pack,. is still in beta, but aims to eventually upgrade all of Deus Ex's item and character textures.
HDTP beta releases, which must be installed over an existing install of HDTP Release 1 (the previous link.)
ModDB link for a compiled installer for the first 3 HDTP beta packs from the previous link.
Chris Dohnal's updated rendering engines for Direct3D9 and OpenGL. As mentioned, the updated renderer for OpenGL is also included with New Vision.
Mission Mods/Total Conversions (These can be installed any time)
Deus Ex: ZODIAC, by Steve Tack, is a side-story to Deus Ex detailing Paul Denton dealing with a splinter group of Majestic 12.
The Nameless Mod is a total conversion which took Off Topic Productions about seven years to finish. With two complete storylines, The Nameless Mod stays true to Deus Ex by offering you multiple ways to do basically everything.
Project 2027 is a fan-made prequel. (I haven't played much of this.) (NOTE: Project 2027 includes its' own launcher, which then calls a copy of DeusEx.exe. You can replace this with Kentie's launcher, but it will be impossible to set any flags on it. Additionally, if you try to launch 2027 via Steam, the menu text will be garbled and impossible to read.)
The Malkavian Mod is a one-map joke mod which creates surreal and hilarious new dialogue via sentence mixing.
Deus Ex Revision is a set of new maps for Deus Ex's storyline, based on the original maps but much expanded.
Modern(ish) Combat is a set of minor modifications to the storyline maps to accommodate the addition of a number of real-life modern weapons. Author recommends using Deus Ex Enhanced.
Gamma Resetter - Used to fix the gamma correction on your screen when Deus Ex crashes and leaves it jacked up.
UI Size Fix, which fixes the scaling of the interface when used at high resolutions. (Included with Kentie's Launcher.)
DXM Labs patch for the .DX map files to update them to the June 2001 versions, from Deus Ex v1110; due to archival problems, the versions of the maps in v1112fm (the GOTY edition, distributed here) are from May 2001.
My personal mirror of the DXM Labs map patch in case the site goes down.
(DEPRECATED?) A slightly modified version of 03_NYC_Airfield.dx, necessitated by a conflict with Kentie's launcher in the original version of the map that causes it to crash shortly after loading. (This should now be only necessary with older revisions of Kentie's launcher; I played the entire map start-to-finish on the retail version of this maps in my latest playthrough and had no problems.)
DarkRealityX's Google Site, which I pulled a number of files in this post from. Includes some good information.
Note: Deus Ex retail does not function properly with multi-co processors; I recommend using the Windows Task Manager and setting the DeusEx.exe process to use only one core. (Right-click DeusEx.exe in the Processes tab and select "Set Affinity...") I don't know if Kentie's Deus Exe has the same problem.
That's all I have for now. Feel free to post stuff and I'll add it later.