Assisting with troubleshooting my 100 slot

Before I ask my question, I want to share with you with my current setup:

Hosting with AllGamer.net on a dedicated server:
Xeon 2.93Ghz
12GB of RAM
Single 250GB HDD
100/100Mb Connection
Running Windows Server 2008 R2 Standard

Minecraft Setup:
Running MCMyAdmin with the latest rec bukkit build
8GB dedicated to the server at 100 slots
5 worlds

Plugins installed (bold if running SQL or web services):

bShortcut
BukkitContrib
BukkitVote
Citizens
ClearInventory
CraftBook
dynmap
Essentials
HeavenActivity
HeroicDeath
HeroSpawn
iChat
iConomy
iConomyChestShop
Landmarks
LogBlock
LoginMessage
LWC
MCDocs
MCMA_compat
MultiInv_2.3.0
MultiVerse
NoCheat
Permissions
PermissionsPlus
SpyerAdmin
Statistician
Superpickaxe
Tables
Vanilla
WorldEdit
WorldGuard

My question:

How are major servers achieving 100+ active members with bukkit even when my server is running on nice hardware but cannot hit 30 without lagging out?

Symptoms:

Once users reach up to 20, server spams lag warnings. People are complaining of block lag, noticeable time lag with the mobs and movement of the environment and chat. Server is not under any CPU load (at 20-30 percent) and RAM is not maxed. People lagging and server freezing when users login.

What I have done troubleshooting so far is turning off mobs. That helps with the client side lag but the server will still throw warnings. Less people complain on chat and block lag after I do that.

My thoughts (I want some to confirm my logic and maybe assist with my troubleshooting):

I believe its the SQL loggers lagging the server because it gets bogged down on queries.

Secondly, is it bad to host on a windows box? Should I be hosting purely on a linux machine to achieve the best situation for 100+ active members?

Is my single 250GB sata hard drive slowing me down?

Also curious if MCMyAdmin has some optimization to help the performance of this program if anyone has any tips and tricks. If it comes down to buying a better server, I will and can upgrade the processor to a dual Xeon but I hate doing so if the server is not under any load.

Appreciate the assistance in helping me achieve a better situation for my server.

 

How do you launch it?

 

MCMyAdmin launches the bukkit.jar within its program: http://mcmyadmin.com/