Some of the things I've used:
- Put the minis for your encounters in zip-loc bags when your doing your game planning session for faster access during the game.
- Index cards numbered 1-20. Give the person with the highest initiative card #1, and #2 goes to the next, etc. Put the cards for the monsters next to the stat blocks. Then everyone simply goes in order from #1 to #20.
- All monsters take 10 for their initiative (BBEG's should roll, minions should definitely "take 10"). Characters can take 10 or take what they roll on d20 (if it's important to go first for some reason). On the player's side, they will always then know when their turn is next.
Personally, I use fantasy grounds to track most of my player's stats, initiative, make die rolls and the like (even though we're doing face-to-face gaming), and I find it helps speed up any game I run having all that info at my fingertips. Yay laptops!