Some things, like car colors and handling, weapons characteristics, ped relations, can be changed easily because all the data necessary stored in plain-text files, with basic guidelines for their usage from game developers in file headers. However, creating more advanced modifications (such as entire buildings or cars) is trickier, and usually requires some advance experience in creating models for games. Google SketchUp is a good program for creating building models. 3DS Max, Lightwave and Zmodeller are also used. Textures creation is also not so simple, textures must match with specific game engine limitations and should be organized by special order into TXD files.
The mission modifications are even harder to produce. First, mission script for game must present in compiled form, which require use of special compiler/decompiler tools for any changes. Second, script language not officially documented, worse, each script editor have own interpretation of it. Finally, many script features depend on hardcoded functions in game executable, which can lead to unexpected troubles with different usage approaches, game region versions, official patches and even depends on end-user hardware. These results with mission modifications are usually simple gameplay missions. Most often used mission script editor is Mission Builder by Barton Waterduck and its derivative, Sanny Builder.
For Total Conversions, even more specific tools needed, like ped & traffic paths editor, GXT (texts) editor, interface (menu) editor and so on. It is strongly advised that you do not attempt to do more than you are capable of. Do not expect to be able to recreate your favorite car in a few hours, many modifications take months.
Vice City Mod Manager or VCMM, is a tool for modifying objects in Grand Theft Auto: Vice City. VCMM uses its own file format VCM, and mods can be downloaded in this format from many different websites.