List at current is based on my own experimentation. There are likely various holes in it since, well, I don't own every Source Engine game.

I've tried to exclude information about decompiling/recompiling projects except where absolutely vital, instead focusing on the raw files included with the game.

List does not include any console versions, since all but one of them (Hybrid) are also on the PC and their formats are typically very different on account of *~*~endians~*~*.

If you have any information that can fill gaps in this list, please post in the comments! I want to make this list more or less definite.

REMEMBER: The Source Engine is a fickle and bipolar mistress even before considering that SFM is a beta-quality internal tool. Your milage can and will vary, often at random, based on your computer specs and dumb blind luck.

Most mods on ModDB and their ilk should work with minimal issues as long as they were built for a post-Orange Box version of Source SDK and their maps were compiled with HDR.

Some mods that are on Steam may have varying compatiblity issues for whatever reason. Here's what I've compiled so far:

Maps do not have HDR compiled. I've fixed all but one of them.[thekinsie.com]

Maps don't seem to work for some strange reason. I'm working on fixing them, but there's a couple of stragglers and weird issues.

Most content is downloadable from within SFM!

Incompatible - Earlier model format

Incompatible - Earlier map format

None yet. The Bloodlines Resurgence Mod had something cooking, but it was cancelled on account of engine frustrations. If you can find the last development release you might be able to scrape something together using the included conversion tools. Good luck!

Included with Source Filmmaker!

Incompatible - Maps load but do not include HDR lighting.

The mod Half-Life 2 Update contains HDR versions of all the HL2 maps that need their cubemaps rebuilt (turn off mat_specular first to fix the glowy rainbow crap)

You might also want the Water Material Fix[drive.google.com]

Fully Compatible
"Valve Artists" uploads in the Workshop may be bugged - extract from VPKs

Semi-Compatible: Episode 2 maps seem to crash a lot.
Lost Coast is fully compatible, but the water material needs to be rejigged for SFM

None

Fully compatible.
Chrome materials need to be rejigged

Incompatible - Maps load but do not include HDR lighting.

None

Fully compatible.

Militia, Dust, Dust2, Inferno, Nuke and Train are compatible.
All other maps are incompatible due to no HDR lighting.

Recompiled maps here.[sfmlab.com]

Fully compatible.
You can download all the DOD content from within SFM!

Fully compatible.
Some detail sprites (grass) conflict with TF2's, causing visual oddities.

The "DLC for SFM" version of these resources includes a mod with an alternate gameinfo.txt to load DOD content before TF2.

Partially Compatible - Flexes may be broken

Incompatible - Maps load but do not include HDR lighting.

SCPH7503 HDR-ized the Arena Mode maps.[filesmelt.com]

Partially Compatible - Flexes may be broken

Incompatible - Different map version

None.

Fully compatible

Semi-Compatible - fancy LUA skyboxes will just display a wireframe graphic over black.

Put the following line in usermod/cfg/autoexec.cfg to allow SFM to load larger custom GMod maps:
Use the console command "sv_skyname (2d skybox name)" to change the skybox material to something nicer.

Partially Compatible - Flexes may be broken

Incompatible - Maps crash on load

A recompiled map pack[dl.dropboxusercontent.com] is available.

Incompatible - Different model format
Models in the official Garry's Mod Model Pack[forums.aceteam.cl] work perfectly

Incompatible - Maps crash on load (and are mostly model based so getting them to work is mostly a lesson in futility)

None.

Fully compatible, apparently.

Untested, please provide feedback!

None.

Semi-compatible - Messed up model headers can cause crashes
L4D2 survivor models are included with SFM!
Repaired L4D1 and 2 models can be downloaded from within SFM!

L4D1 is compatible.
L4D2 tends to crash a lot.

This compatibility fix helps a lot when using the raw retail files, and includes fixed maps.
Fixed DLC maps here[sfmlab.com].

The DLC seems to be missing a lot of prop materials from the game. You can copy these over from the L4D2 VPKs just fine - just copy the folders in materials/models/ that start with "props_" over to the appropriate L4D2 DLC folder and don't overwrite anything. Sorted!

Included with Source Filmmaker!

Included with Source Filmmaker!
The CP and KOTH versions of Badlands are haunted and will not work. I have no idea why this is.

MVM maps require a manual update to the latest TF2 files to look right

Fully compatible.
Portal 2 models and audio can be downloaded from within SFM!

Fully compatible.
Portal 2 maps may require Draw Game Entities > Draw Other Entities due to number of props making up environment

None.

Semi-compatible - Player models have messed up model headers and can cause crashes

Incompatible - Maps crash upon load, some are just too big for SFM to handle

None.

Almost Compatible - models need processing with bat file (see Fixes)

Fully Compatible.
May crash if you view too much of the map at once due to no distance clipping.
Also, erm, no ceiling. You'll have to work around that too.

You'll need to use the model fixer bat file[dl.dropboxusercontent.com] to get models working.

Modified map files[sfmlab.com] to fix the crashing issue.

Fully compatible.
Unusual player model bone setup makes IK rigging difficult...

Incompatible? Need testing!

Recompiled maps can be found here.[dl.dropboxusercontent.com] Sadly I have no idea who fixed them - their identity was lost with SFMBox.

Fully compatible.

Partially compatible - Envmaps are a rainbow mess (turn mat_specular off before running buildcubemaps to fix)

In progress.

Fully compatible.
Some of these can be downloaded from within Source Filmmaker!

Fully compatible.

None.

Untested, please provide feedback!

Untested, please provide feedback!

None.

Fully compatible.

Incompatible - Modified map format... kind of killing the whole point, really.

Recompiled maps can be found here.[facepunch.com]

Incompatible - Tragicomic developer incompetence

Incompatible - Modified map format

None.

Untested, please provide feedback!

Untested, please provide feedback!

None.

Fully compatible.
Extracting the game data requires a little trickery[facepunch.com] due to a different VPK format header throwing GCFScape off.

Incompatible - Maps are encrypted and crash on loading.

Recompiled maps here.[thekinsie.com]

Fully compatible.
Custom shaders are used that may not look right (wireframes, odd colours etc.) unless you edit the VMT files.

Incompatible - different map format.

Individual models can be decompiled and recompiled.
Maps can be decompiled and recompiled.

Partially compatible - Redone player models tend to be messed up.

Incompatible - Different map lighting format.

Recompiled maps here.[sfmlab.com]
Updated player models here.

Fully compatible.
Weird shaders are used that may not look right under non-Dota circumstances.

Incompatible - Different map format.

Recompiled maps here.[sfmlab.com]

Fully compatible.
Player and weapon models and audio can be downloaded from within SFM!

Mostly Compatible except for duel_temple, which crashes SFM when loading.
Fixed SFM-specific versions can be downloaded from within SFM!

The official VMF files for recompiling and editing the maps are available on Puny Human's GitHub[github.com]. SFM-centric VMFs are here[github.com].

Fully compatible.
Many models are reskinned from Portal 2, so if both games are mounted they may not look as you remember.
You can download all the TSP content from within SFM!

Everything except the Minecraft map is compatible.
Some maps may not look as you remember due to heavy abuse of scripted portalling in TSP.
You can download the main TSP map from within SFM!

None.

Not compatible - Slightly different model format, LZMA-compressed materials

Not compatible - different format?

None... yet.

Fully compatible!

Incompatible

A couple of recompiled maps here.[drive.google.com]

Partially Compatible - Some player models have the wrong headers, causing crashes. Easily fixable with hexing.
Custom shader is used for weapon materials, causing them to look like wireframes unless you edit the VMT files.

Incompatible - Raised entity limits result in maps too detailed for SFM.

A couple of recompiled maps here.[thekinsie.com]

Semi-compatible - models work fine, material VMTs all need rejigging due to fancy deferred rendering system in Consortium.

Not compatible - deferred lighting system and generally way too much STUFF for poor old vanilla Source to chew on.

You can get things visible and non-wireframe-y by find-replacing "DEFERRED_MODEL" with "VertexLitGeneric" and "DEFERRED_EYES" with "Eyes", but further tweaks are needed to make the model shading better imitate the original game.

Kind of vaguely compatible if you squint a bit - incompatible normal map format, broken rigging and animations, that kind of thing.

Extremely incompatible.

Models: Use VPKTool[dev.cra0kalo.com] to extract and Crowbar to decompile and recompile for the SFM version of the engine. Watch this space[facepunch.com] for further tools and fixes and possibly pre-fixed content!
Maps: lmbo

Untested, please provide feedback!

Untested, please provide feedback!

None.

Fully compatible!

Incompatible.

Official Map VMF Files Are here[drive.google.com]