It should be noted that normally, the program lacks a speed-limiting feature in windowed mode, so it runs far too fast on modern PCs. However, you can specify a framerate to run at, which is explained further here. The timings used by full screen mode are always based on the monitor's refresh rate, so the game can always be played correctly on a modern system as long as your refresh rate is set to 60Hz.
Most of the original music is emulated, with the user able to choose between MIDI and FM formats. Furthermore, some of Sonic 3's music tracks in US and EU versions, including those of Carnival Night Zone, IceCap Zone, Launch Base Zone, Knuckles' theme, the Competition menu, and the credits music, were replaced with original compositions. One possible explanation for this is that the tracks featured sampled sound effects not supported by the MIDI standard, and some sound cards during this time were not capable of playing these alongside the standard MIDI instruments. Another potential explanation is that the original tracks may have been composed by Michael Jackson, and were replaced to original soundtrack due to legal reasons that arose since their original release. IceCap Zone's soundtrack may have been replaced due to having its origins in Hard Times, an unreleased 1982 track by The Jetzons, an American new wave band whose keyboardist, Brad Buxer, later worked on the Sonic 3 soundtrack. Aside from this musical difference, the game plays virtually identically to its original incarnations.
Other differences include the fact that the Sonic 3 & Knuckles Level Select Cheat works on Sonic 3 alone, in Angel Island Zone. This code (usually input at Mushroom Hill Zone in Sonic & Knuckles) does not enable debug mode as in the original, though it does still allow characters to play stages they couldn't access otherwise from the level select. Examples include Tails in Doomsday Zone and Knuckles in Sky Sanctuary 1. When the level select code is performed in Sonic 3, and the first special stage option is selected (which unlike in the original accesses the blue sphere mini-game), this enables the player to use Knuckles in the Sonic 3 levels, though they are incomplete and thus cannot always be beaten.
Sonic the Screen Saver
In the US and in Europe, "Sonic the Screen Saver" was included in the compilation. This disc allowed users to customize Windows with Sonic themes, wallpapers, icons, and play music from Sonic 1, 2, 3, S&K and the Japanese version of Sonic CD. In Japan, Sonic the Screen Saver was sold separately.