This page is a big list of mappers which MESS does, doesn't, or partially supports.

If you find a cart which does not load in MESS and you want to find out if it's due to an unsupported mapper, run

mess.exe -log

and take a look to error.log, which could contain useful info.

info from gb.c

Name of mapper	Game(s) which use this	Documented?	Supported in MESS?
MBC1 Mapper	?	Yes	Yes
MBC2 Mapper	?	Yes	Yes
MBC3 Mapper	?	Yes	Yes
MBC4 Mapper	?	?	No
MBC7 Mapper	Kirby's Tilt n' Tumble, Command Master	?	Partial support
TAMA5 Mapper	Tamagotchi 3	?	Partial support
MMM01 Mapper	Momotarou Collection 2, Taito Pack	?	No
HuC1 Mapper	?	?	No
HuC3 Mapper	?	?	No
Wisdom Tree Mapper	?	?	?

info from genesis.c

Game(s) “mapper”	Documented?	Supported in MESS?
Super Street Fighter 2		Yes
Lion King 3		Yes
Super King Kong 99		Yes
Super Donkey Kong 99		Yes
Romance of the Three Kingdoms - Battle of Red Cliffs (decoded)		Yes
Romance of the Three Kingdoms - Battle of Red Cliffs (.mdx)		Yes
Radica TV games		Yes (maybe better as separate driver)
King of Fighters '99		Yes
Soul Blade		Yes
Mahjong Lover		Yes
Squirrel King		Yes
Smart Mouse		Yes (but 1572)
Super Mario Bros.		Yes
Super Mario Bros. 2		Yes
Kaiju? (Pokemon Stadium)		Yes
Chinese Fighters 3		Yes
Lion King 2		Yes
A Bug's Life		Yes
Elf Wor		Yes
Rockman X3		Yes
Super Bubble Bobble		Yes
King of Fighters '98		Yes
Whac a Critter/Mallet legend, Defend the Earth, Funnyworld/Ballonboy		Yes
Super 19 in 1		Yes
Super 15 in 1		Yes
Games above need ad hoc memory bank initialization. There may exist many other ones.

info from c64.c

Mapper #	Game(s) which use this	Documented?	Supported in MESS?
00	Generic 8/16 Kb cartridges	Yes	Yes
01	Action Replay	Yes	No
02	KCS Power Cartridge	Yes	No
03	Final Cartridge III	Yes	No
04	Simons Basic	Yes	No
05	Navy Seals, Robocop 2 & 3, Shadow of the Beast, Toki, Terminator 2 and more. Both 256 and 128 Kb images.	Yes	No
06	Expert Cartridge	Yes	No
07	Fun Play, Power Play	Yes	No
08	Super Games	Yes	No
09	Atomic Power	Yes	No
10	Epyx Fastload	Yes	No
11	Westermann Learning	Yes	No
12	Rex Utility	Yes	No
13	Final Cartridge II	Yes	No
14	Magic Formel	Yes	No
15	C64 Game System, System 3	Yes	No
16	WarpSpeed	Yes	No
17	Narco Police and more	Yes	No
18	Zaxxon, Super Zaxxon (SEGA)	Yes	No
19	Magic Desk, Domark, HES Australia	Yes	No
20	Super Snapshot 5	Yes	No
21	Comal-80	Yes	No
22	Structured Basic	Yes	No
23	Ross	Yes	No
24	Dela EP64	Yes	No
25	Dela EP7x8	Yes	No
26	Dela EP256	Yes	No
27	Rex EP256	Yes	No
28	Mikro Assembler	Yes	No
29	Final Cartridge I	Yes	No
30	Action Replay 4	Yes	No
31	StarDOS	Yes	No
All mappers are properly documented here
Known Issues: Addition of more mappers to MESS has been requested 1558. Also, Carts with more than 32 memory banks currently crash at load 1488.

info from snescart.c

Chip	Game(s) which use this	Documented?	Supported in MESS?
DSP-1	Super Mario Kart, Pilotwings, others	Yes	Yes
DSP-2	Dungeon Master	Yes	Yes
DSP-3	SD Gundam GX	Partial	Yes
DSP-4	Top Gear 3000	Partial	Yes
Super FX / FX2	Star Fox, Super Mario World 2: Yoshi's Island, others	Yes	Yes
SA-1	Super Mario RPG, Kirby's Dream Land 3, others	Yes	No
SDD-1	Star Ocean, Street Fighter Alpha 2	Yes	Yes
OBC-1	Metal Combat: Falcon's Revenge	Yes	Yes
S-RTC	Dai Kaiju Monogatari 2	Yes	Partially
Z80GB	Super Game Boy	Yes?	No (*)
C4	Mega Man X2, Mega Man X3	Yes	Yes
Seta ST-010	F1 ROC II: Race of Champions	Yes?	Yes
Seta ST-011	Hayazashi Nidan Morita Shogi	Yes?	No
Seta ST-018	Hayazashi Nidan Morita Shogi 2	Yes?	No
SPC7110	Momotaro Dentetsu Happy, Super Power League 4	Yes	Partially
SPC7110 + RTC	Far East of Eden Zero	Yes	No
(*) it's partially implemented in a separate driver

info from nes_ines.c & nes_unif.c

INES #	Name of mapper	Game(s) which use this	Documented?	Supported in MESS?	Known Issues
0	No Mapper	Mario Bros., Super Mario Bros., Tennis, etc.	?	Yes	-
1	MMC1	Legend of Zelda, Metroid, Kid Icarus, Final Fantasy, etc.	?	Yes	-
2	74161/32 ROM sw	Castlevania, Dragon Quest II, Metal Gear, MegaMan, Duck Tales, etc.	?	Yes	-
3	74161/32 VROM sw	Gradius, Hokuto no Ken, Adventure Island, etc.	?	Yes	-
4	MMC3	Final Fantasy III, Super Mario Bros. 2 & 3, MegaMan 3, 4, 5 & 6, etc.	?	Yes	-
5	MMC5	Castlevania III, Just Breed, etc.	?	Partially	Has many issues
6	FFE F4xxxx	?	?	Yes	Not Widely Tested
7	ROM Switch	Arch Rivals, Commando, Battletoads, Solstice, etc.	?	Yes	-
8	FFE F3xxxx	?	?	Yes	Not Widely Tested
9	MMC2	Punch Out!, Mike Tyson's Punch Out!	?	Yes	-
10	MMC4	Famicom Wars, Fire Emblem, Fire Emblem Gaiden	?	Yes	-
11	Color Dreams Mapper	?	?	Yes	-
12	Rex Soft Bootleg Board	Dragon Ball Z 5, Dragon Ball Z Super	?	Yes	-
13	CP-ROM	Videomation	?	Partially	Needs banked VRAM
14	SL1632	Samurai Spirits	?	Yes	-
15	Waixing Bootleg Board	Bao Xiao Tien Guo, Bio Hazard, Pokemon Gold, etc.	?	Yes	-
16	Bandai LZ93D50 (+24C02)	Dragon Ball Z 2 & 3, Dragon Ball Z Gaiden, Rokudenashi Blues, etc.	?	Yes	missing 24C02 EEPROM emulation
17	FFE F8xxx	?	?	Yes	Not Widely Tested
18	Jaleco SS88006	Ninja Jajamaru, Pizza Pop, Plasma Ball, etc.	?	Yes	-
19	Namco 163 & 163S	Family Circuit '91, Famista '90, '91, '92 & '94, Wagyan Land 2 & 3, etc.	?	Yes	-
20	Famicom Disk System	?	?	Yes	No image should use this mapper. Disks should use .fds format
21	Konami VRC4A & VCR4C	Ganbare Goemon Gaiden 2, Wai Wai World 2, etc.	?	Yes	-
22	Konami VRC2A	Ganbare Pennant Race, Twin Bee 3	?	Yes	-
23	Konami VRC2B	Getsufuu Maden, Parodius Da!	?	Yes	-
24	Konami VRC6A	Akumajou Densetsu	?	Yes	-
25	Konami VRC4B & VCR4D	Bio Miracle Bokutte Upa, Ganbare Goemon Gaiden, TMNT 1 & 2 Jpn, etc.	?	Yes	-
26	Konami VRC 6B	Esper Dream 2, Mouryou Senki Madara	?	Yes	-
27		World Hero	?	No	-
28	-	-	-	-	-
29	-	-	-	-	-
30	-	-	-	-	-
31	-	-	-	-	-
32	Irem G101A & G101B	Image Fight, Kaiketsu Yanchamaru 2, Maikyuu Shima, Paaman, etc.	?	Yes	-
33	Taito TC0190FMC	Akira, Bakushou!! Jinsei Gekijou, Don Doko Don, Insector X, Power Blazer, etc.	?	Yes	-
34	Nina-1	Deadly Tower, Impossible Mission II, Titanic 1912, Dance Xtreme	?	Yes	-
35	SC-127	Wario World II (Kirby Hack)	?	Yes	-
36	TXC Bootleg Board	Strike Wolf	?	Yes	-
37	ZZ Board	Super Mario Bros. + Tetris + Nintendo World Cup (E)	?	Yes	-
38	Discrete Logic Board	Crime Busters	?	Yes	-
39	Subor Bootleg Board	Study n Game 32 in 1	?	Yes	-
40	Unknown Bootleg Board	Super Mario Bros. 2 Pirate (Jpn version of SMB2)	?	Yes	-
41	Caltron Board	Caltron 6-in-1	?	Yes	-
42	Unknown Bootleg Board	Mario Baby	?	Yes	-
43	150-in-1 (?)	?	?	Maybe (?)	-
44	Unknown Multigame Bootleg Board	Kunio 8 in 1, Super Big 7 in 1	?	Yes	-
45	Unknown Multigame Bootleg Board	Street Fighter V, various multigame carts	?	Yes	-
46	Rumblestation Board	Rumblestation 15 in 1	?	Yes	-
47	QJ Board	Super Spike V'Ball + Nintendo World Cup	?	Yes	-
48	Taito TC0190FMC PAL16R4	Bubble Bobble 2, Captain Saver, Don Doko Don 2, Flintstones, etc.	?	Yes	-
49	Unknown Multigame Bootleg Board	Super HIK 4 in 1	?	Yes	-
50	Unknown Bootleg Board	Super Mario Bros. 2 Pirate (Jpn version of SMB2)	?	Yes	-
51	Unknown Multigame Bootleg Board	11 in 1 Ball Games	?	Partially	Only half of the games work
52	Unknown Multigame Bootleg Board	Mario 7 in 1	?	Yes	-
53	Unknown Multigame Bootleg Board	Supervision 16 in 1	?	No	-
54	Unknown Multigame Bootleg Board	None, but this corresponds to a UNIF board	?	Yes	-
55	Bootleg Board	?	?	-	Mentioned in NEStopia source. More info needed.
56	KS202	Super Mario Bros. 3 Pirate	?	Yes	-
57	Unknown Multigame Bootleg Board	6 in 1, 54 in 1, 106 in 1	?	Yes	-
58	Unknown Multigame Bootleg Board	68 in 1, 73 in 1, 98 in 1	?	Yes	-
59	-	-	-	-	-
60	Unknown Multigame Bootleg Board	4 in 1, 35 in 1	?	No	These are Reset-based games and we still do not support them
61	RCM Bootleg Board	Tetris Family 9 in 1, 20 in 1	?	Yes	-
62	Unknown Multigame Bootleg Board	Super 700 in 1	?	Yes	-
63	Bootleg Board	?	?	-	Mentioned in NEStopia source. More info needed.
64	Tengen 800032	Klax, Road Runner, Rolling Thunder, Shinobi, Skulls & Croosbones, Xybots, etc.	?	Partially	Has many IRQ problems
65	Irem H3001	Daiku no Gen San 2 - Akage no Dan no Gyakushuu, Kaiketsu Yanchamaru 3, Spartan X 2	?	Yes	-
66	74161/32 Jaleco	?	?	?
67	SunSoft 3	?	?	Display issues, but vrom fixed
68	SunSoft 4	?	?	?
69	SunSoft 5	?	?	?
70	74161/32 Bandai	?	?	(ark2j) starts on round 0 - is this right? Yep!
71	Camerica	?	?	?
72	74161/32 Jaleco	?	?	?
73	Konami VRC 3	?	?	?
74		?	?	?
75	Konami VRC 1	?	?	?
76	Namco 109	?	?	?
77	74161/32 ?	?	?	?
78	74161/32 Irem	?	?	?
79	Nina-3 (AVE)	?	?	?
80	Taito X1-005	?	?	?
81		?	?	?
82	Taito C075	?	?	Has chr-rom banking problems. Also mapper is in the middle of sram, which is unemulated.
83	Cony	?	?	?
84	Pasofami	?	?	?
85	Konami VRC 7	?	?	?
86	Jaleco Early Mapper 2	?	?	?
87	74161/32 VROM sw-a	?	?	?
88	Namco 118	?	?	?
89	Sunsoft Early	?	?	?
90	Pirate mapper	?	?	?
91	HK-SF3 (bootleg)	?	?	?
92	Jaleco Early Mapper 1	?	?	?
93	Sunsoft LS161	?	?	?
94	Capcom LS161	?	?	?
95	Namco ??	?	?	?
96	74161/32	?	?	Preliminary
97	Irem - PRG HI	?	?	?
98		?	?	?
99	vs. system	?	?	?
100	Images hacked to work with nesticle	?	?	?
101	?? LS161	?	?	?
102		?	?	?
103		?	?	?
104		?	?	?
105	?	Nintendo World Championship	?	No
106		?	?	?
107		?	?	?
108		?	?	?
109		?	?	?
110		?	?	?
111		?	?	?
112	Asper	?	?	?
113	Sachen/Hacker/Nina	?	?	?
114		?	?	?
115	Bao Qing Tian	?	?	?
116		?	?	?
117	?	San Guo Zhi 4	?	No 923
118	MMC3?	?	?	Mirroring is a guess, chr-rom banking is likely different
119	MMC3	High Speed, Pinbot	?	No 923
120		?	?	?
121		?	?	?
122		?	?	?
123		?	?	?
124		?	?	?
125		?	?	?
126		?	?	?
127		?	?	?
128		?	?	?
129		?	?	?
130		?	?	?
131		?	?	?
132		?	?	?
133	Sachen	?	?	?
134		?	?	?
135		?	?	?
136		?	?	?
137		?	?	?
138		?	?	?
139		?	?	?
140	Jaleco	Bio Senshi Dan	?	No 923
141		?	?	?
142		?	?	?
143		?	?	?
144	AGCI 50282	?	?	?
145		?	?	?
146		?	?	?
147		?	?	?
148		?	?	?
149		?	?	?
150		?	?	?
151		?	?	?
152		?	?	?
153		?	?	?
154		?	?	?
155		?	?	?
156		?	?	?
157		?	?	?
158		?	?	?
159		?	?	?
160		?	?	?
161		?	?	?
162		?	?	?
163		?	?	?
164		?	?	?
165		?	?	?
166		?	?	?
167		?	?	?
168		?	?	?
169		?	?	?
170		?	?	?
171		?	?	?
172		?	?	?
173		?	?	?
174		?	?	?
175		?	?	?
176		?	?	?
177		?	?	?
178		?	?	?
179		?	?	?
180	Nihon Bussan - PRG HI	?	?	?
181		?	?	?
182	Super games	?	?	?
183		?	?	?
184	Sunsoft VROM/4K	?	?	?
185	?	Banana, Mighty Bomb Jack, and Spy vs. Spy	?	No 923
186		?	?	?
187		?	?	?
188	UNROM reversed	?	?	?
189		?	?	?
190		?	?	?
191		?	?	?
192		?	?	?
193	Fighting Hero	?	?	Missing PPU feature?
194		?	?	?
195		?	?	?
196		?	?	?
197		?	?	?
198		?	?	?
199		?	?	?
200	X-in-1	?	?	?
201	X-in-1	?	?	?
202	150-in-1	?	?	?
203	35-in-1	?	?	?
204		?	?	?
205		?	?	?
206	MMC3 no mirror	?	?	?
207		?	?	?
208		?	?	?
209		?	?	?
210		?	?	?
211		?	?	?
212		?	?	?
213		?	?	?
214		?	?	?
215		?	?	?
216		?	?	?
217		?	?	?
218		?	?	?
219		?	?	?
220		?	?	?
221		?	?	?
222		?	?	?
223		?	?	?
224		?	?	?
225	72-in-1 bootleg	?	?	?
226	76-in-1 bootleg	?	?	?
227	1200-in-1 bootleg	?	?	?
228	Action 52	?	?	Seems wrong
229	31-in-1	?	?	Preliminary
230	22-in-1	?	?	No
231	Nina-7 (AVE)	?	?	?
232	Quattro	Quattro Arcade	?	No 923
233		?	?	?
234	Maxi-15	?	?	?
235		?	?	?
236		?	?	?
237		?	?	?
238		?	?	?
239		?	?	?
240	Jing Ke Xin Zhuan	?	?	?
241	Education 18-in-1	?	?	Preliminary
242	Wai Xing Zhan Shi	?	?	?
243		?	?	?
244	?	Decathlon	?	No 923
245		?	?	?
246	Fong Shen Bang	?	?	?
247		?	?	?
248		?	?	?
249		?	?	?
250		?	?	?
251		?	?	?
252		?	?	?
253		?	?	?
254		?	?	?
255		?	?	?

UNIF Name of Board	Game(s) which use this	Documented?	Supported in MESS?	Correspondent Mapper
BMC-64IN1NOREPEAT	64-in-1 Y2K	?	Yes	None
BMC-190IN1	190-in-1	?	Yes	None
BMC-A65AS	3-in-1 (N068)	?	Yes	None
BMC-GS2004	Tetris Family 6-in-1	?	Preliminary	None
BMC-GS2013	Tetris Family 12-in-1	?	Preliminary	None
BMC-NOVELDIAMOND9999999IN1	Novel Diamond 999999-in-1	?	Yes	54
BMC-SUPER24IN1SC03	Super 24-in-1	?	Yes	None
BMC-T-262	4-in-1 (D-010), 8-in-1 (A-020)	?	Yes	None
BMC-WS	Super 40-in-1	?	Yes	None
DREAMTECH01	Korean Igo	?	Yes	None
UNL-8237	Pochahontas 2	?	Preliminary	None
UNL-AX5705	Super Mario Bros. Pocker Mali	?	Yes	None
UNL-CC-21	Mi Hun Che	?	Yes	None
UNL-KOF97	King of Fighters 97 (Rex Soft)	?	Preliminary	None
UNL-SC-127	-	?	Yes	35
UNL-T-230	Dragon Ball Z IV (Unl)	?	Yes	None