Heh. All of them! Depends on whether you want to customise them yourself or do you mean Mod Quanitity?
As a general rule older popular games have more mods than recent new ones so UnrealTournament99 and Counter Strike will have more than say Supreme Commander, also different games have different "Customisations".
Some games have Aesthetic mods like HUD makeovers and tweaks to colours and textures like Oblivion has the majority of, others have Gameplay mods like extra content or new game modes like BunnyTracking for UT or CSS SCIFI (Counterstrike mixed with HL2DM).
Bewary of GameBreakers though, some people really dont care how they mod a game and whle fun can ultimately spoil it, ie Modifying a weapon or item to have a stupidly extravagant or strong effect such as the Magnum Nuke in CS1.7.
My list of Modifiable games(quality) are as follows :
Unreal Tournament 99 + 2004 - Bunnytrack, Custom Maps,Skins, Audio Samples and variety of Server configs.
Counter Strike 1.7 - Almost everything thinkable + Hackers... :(
Counter Strike Source
Elder Scrolls 3/4
The Sims 2 (Sims 1 is more or less defunct by Family Based Homicide....)
Half Life 2 : Silly Mod
Command & Conquer :Generals
Also if you are after customising games yourself and are willing to spend ALOT of time learning try;
It is a game/life sim where your real life skills at modding/coding make the environment your avatar lives in. Two people have been recruited into game dev teams because of their work in this world, so its not just XXX shops in a virtual world here.
Oblivion and Crysis look interesting. And Warcraft 3 now that you mention it. That also makes me think of Starcraft since someone said that is a perfect game in their opinion. San Andreas I never really heard about that game before, except that the series is one of the most popular. I didn't know they had mods for it.
My personal style of customization is, I like gameplay that sharpens the mind a little, while still being fun. So I try to mod things that way, or with games like UT3, you can just set up a match at that level of difficulty.