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The first games that could be consider a true tower defense game would be the 1990 atari game "Rampart".  However this games differs from more modern tradition tower defense games in that the towers had to be manually aimed. Most tradition Tower defense games feature automated turrets, that do not need the user to aim them.

What is considered to be the birth of the modern tower defense games as we now see them is considered to be world of warcraft 3.  Players started to create maps specifically to make units run a gambit of turrets. World of warcraft 3 tower defense or simply ,  wc3 tower defense , maps became quite popular and as a result  flash elements tower defense was create as an online flash game. This was followed by perhaps the most popular flash game of all time,  Desktop Tower Defense. Other popular flash games followed such as the Protector series, Xeno TacticsDungeon defender, Warzone tower defense, Bubble tanks tower defense.  The  Bloons tower defense series was the most popular of these earlier tower defence games, with Bloons tower defense 4 being the most popular of the series. 

Bloons Tower Defense 4

Tower defence games became fairly popular, but were primarily played only as free online games using flash on their browser. Some games such as the Bloons tower defense series were offered on the Iphone and android and others followed. Soon some there were tower defense games that were created specifically for other platforms. Defense Grid was created for the PC and xbox360.  Pixel junk monsters and Savage moon for the Playstation 3 and many handheld consoles such as the Nintendo DS had tower defense games created for them.

In the last year, 2010, Tower defense games have seen somewhat of a resurgence. The top ranked game on Kongergate currently is Curse treasures tower defense. However, tower defense games are not as popular as they once were, and many high quality tower defense games such as Ghost hacker tower defense and Germicide Tower defense,  fell through the cracks despite their excellent gameplay. What the future brings for Towerdefense games remains to be seen.

For more info check out wilkipedia's tower defense wiki