As far as X3 is concerned, the bosses were harder than the previous 2 X games and the boss designs were probably some of the best in the series.
with that:
1. Super Mario World
2. The Adventures of Batman and Robin
3. Killer Instinct
4. Wild Guns
5. Street Fighter II Turbo
6. Sparkster
7. Demon's Crest
8. Battletoads in Battlemaniacs
9. Assault Suits Valken/Cybernator
10. Legend of Zelda: A Link to the Past
11. Jikkyou Oshaberi Parodius
12. Animaniacs
13. Yu Yu Hakusho Final
14. Imperium
15. Star Fox
16. The Illusion of Gaia
17. Super Metroid
18. Megaman X
19. Super Ghouls N' Ghosts
20. Chrono Trigger
21. Final Fight 3
22. Super Mario World 2: Yoshi's Island
23. Actraiser
24. Ranma ½ Chougi Ranbu Hen
25. Final Fantasy VI
26. Axelay
27. Ninja Warriors Again
28. Super Mario RPG Legend of the Seven Stars
29. Firepower 2000
30. Donkey Kong Country 2 Diddy's Kong Quest
31. Teenage Mutant Ninja Turtles IV Turtles in Time
32. Undercover Cops
33. U.N. Squadron
34. Battle Clash
35. Zombies Ate My Neighbors
36. Ghost Chaser Densei
37. Harvest Moon
38. X-Men: Mutant Apocalypse
39. Joe & Mac Caveman Ninjas
40. Maximum Carnage (Spider-Man & Venom)
41. F-Zero
42. Terranigma
43. Donkey Kong Country
44. Hagane The Final Conflict
45. Super Castlevania IV
46. SunSet Riders
47. Kirby Super Star
48. Marvel Super-Heroes: War of the Gems
49. Contra III: The Alien Wars
50. Run Saber
51. Earthbound
52. Raiden
53. Soul Blazer
54. Metal Warriors
55. Secret of Mana
56. Death and Return of Superman
57. Rock N' Roll Racing
58. Final Fantasy IV
59. Final Fantasy V
60. Plok
61. Legend of the Mystical Ninja
62. Super Street Fighter II: The New Challengers
63. Gundam Wing: Endless Duel
64. Super Mario Kart
65. E.V.O.: Search for Eden
66. Lost Vikings
67. Gradius III
68. R-Type III: The Third Lightning
69. Mega Man X 3
70. Marvelous: Mōhitotsu no Takarajima
71. Battletoads/Double Dragon
72. Fire Emblem: Monshou no Nazo
73. NBA Jam: Tournament Edition
74. Tiny Toon Adventures: Buster Busts Loose!
75. Jaki Crush
76. Spider-Man & Venom: Separation Anxiety
77. Aladdin
78. Earthworm Jim
79. Super R-Type
80. Panel De Pon/Tetris Attack
81. Super Punch Out
82. Wolfestein 3-D
83. Ogre Battle
84. KABLOOEY!
85. Star Trek: The Next Generation: Future's Past
86. Pocky & Rocky 2
87. The Magical Quest Starring Mickey Mouse
88. Robotrek
89. Aero Fighters
90. Knights of the Round
91. Hook
92. Pilotwings
93. Hamelin no Violin Tamaki
94. Sim City
95. Super Mario All-Stars
96. Castlevania: Dracula X
97. King of Dragons
98. Secret of the Stars
99. Super Star Wars
100. Batman Returns
101. Ninja Gaiden Trilogy
102. Super Famicom Wars
103. Mortal Kombat II
104. Emerald Dragon
105. Street Fighter Alpha 2
106. Super Star Wars The Empire Strikes Back
107. Megaman VII
108. Breath of Fire II
109. Ghoul Patrol
110. Ultimate Mortal Kombat 3
111. Megaman X2
112. BlackThrone
113. Super Star Wars: Return of the Jedi
114. Pocky & Rocky
115. Umihara Kawase
116. ShadowRun
117. Kirby's Dream Course
118. Justice League: Task Force
119. Bubsy
120. Mighty Morphin Power Rangers: Fighting Edition
121. Mighty Morphin Power Rangers
122. Captain Commando
123. Rockman & Forte
124. Arkanoid - Doh It Again
125. Lufia 2: Rise of Sinistrals
126. Mighty Morphing Power Rangers: The Movie
127. Bahamut Lagoon
128. Magic Sword
129. Kunio-kun no Dodgeball
130. Mortal Kombat 3
131. Super Tennis
132. Tetris & Dr. Mario
133. Donkey Kong Country 3: Dixie's Double Trouble
134. S.T.G Strike Gunner
135. Phalanx
136. Secret Of Evermore

If you peel away the negative hype generated by the Squaresoft die-hards who wanted Secret Of Mana 2 and believed that Squaresoft released this instead, you have an avant-garde RPG that brings a lot of innovative ideas to the table, and probably one of the most artistic RPGs on the SNES. What makes the game unique is the environments it's set in. I can't think of any other RPG that has such a vast array of worlds to explore (prehistoric times, ancient egypt/rome, midevil times, and a space station).
The 'spell' system, which is actually an alchemy system is a unique addition. Instead of learning spells through levelling up, you learn alchemy spells through people teaching you the ability. You end up combining elements in order to cast your alchemy spells instead of a magic/PP system. Heck, you even pick up alchemy elements along the entire length of your journey.
And Jeremy Soule composed the entire soundtrack, which is an amazing one at that. IT isn't an elaborate charlie-foxtrot orchestral piece (that the Final Fantasy series is known for), but rather a music-to-fit-the-mood-of-what-is-going-on-at-this-moment soundtrack. I literally play the game for the music and it makes the experience of the game that much more worthwhile.
It's definitely NOT top 100, especially considering the game was rushed through production (and you can certainly tell as the game goes on) and is laden with glitches and has various other issues; but Secret of Evermore is definitely worthy of a spot here