below are a few sites that i use to help run my games. if there are any someone would like to add to this list please do so:
D20 srd (Brew Dragon Recommended) this is a site that i swear by, the tools are great for any d20 system and it has links to a dice roller,monster and spell index, it also has an encounter calculator, this little tool lets a DM calculate Experience, treasure and challenge of the encounter
dungeon mapper yea i know it's wizards of the coast but it's still a great source for basic map ideas
Dungeon mastering this site is for those people who play 4th edition Dungeons. this site has the DM tools. they cost money but if your an advanced DM or just Starting out these tools can help... the cost is $45 after a 5 day free trial.