+1 on
Autoruns, it's a bit hard to understand how much you can turn off until you've tried it. It's much more than what you see in MSConfig, or HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Run or the other \Run.
Personally I use MSConfig just to get an idea of how much is autostarted, then I go to Regedit to disable it, unless I'm just testing, MSConfig is great for turning on or off. So yeah, I like Autoruns, but on my own computer I rarely find anything extra with it that I want to turn off.
Another tool straight from MS is
Windows Performance Toolkit. I've never used it, but it seems like it can improve boot time. Maybe a successor to Bootvis, if anyone remembers that one. I haven't tried it yet so I'm giving you a link to a forum thread, just to give you some feedback to read.
Classic Shell is a must have for me in Windows 7 (and Vista).
It brings back the up button in Explorer, but can also give a full, classic path in the address bar, and classic folder tree.
During install you can also choose to install a Classic Start Menu, but I've never done it because I'm not interested in that.
WinSetupFromUSB is the best tool for copying Windows ISO's to USB memory, although there's a chance you might get lost in all the options, so let me do it simple for you:
1 - Do a quick format of your USB memory in Explorer (NTFS).
2 - Start WinSetupFromUSB, add your ISO of choice.
3 - During the boot countdown, pick the right choice.
Unetbootin is another choice, but it doesn't always play nice with XP or 2003 (use FAT 32 if it doesn't work, helps sometimes). For anything newer it's a very good tool.
Both these works with modified ISO's (think nlite), unlike MS official tool. They work with many other bootable ISO's like Linux etc.
NT 6.x fast installer is useful if you want to install Windows
on a USB drive, just don't try this on a regular USB-memory..

I did, and after five hours Windows 7 was still starting up.
Check out
Scheduled Tasks, I found more than a couple of useless tasks there in W7. I'm not sure if it made much of a difference, but it feels like my laptop got a bit quicker after I disabled some of them. Go through the list, I'm sure you find something meaningless.
I always keep my personal files on a
second partition, even on a single HDD computer. This is NOT because of performance reasons, it's just very convenient to separate personal files from system files.
There's more than one way to do this, but the easiest and fastest is to select the folders you want in C:\Users\Mats\ while holding down Ctrl, then right-click-drag-and-drop them where you want them, then pick "move" in the pop up window. The settings in the registry gets changed automatically. I put them directly into D:\, but if you have more than one account on the computer you should of course put them in separate folders.

Appdata is the only folder I don't move.
After doing this, I can format C:, or reinstall the system image, whenever I want.
Speaking of
System image, that's one more reason not to use system restore. It's a very useful tool in W7.
If you have a virus in the Restore folders, use a third party file explorer to remove them (or if you just want to delete them manually), I actually still use
ExplorerXP, remember to run it in XP compatibility mode, otherwise you can't see the context menus.
Agent Ransack is a good alternative to Windows Search, another one is
Everything.
I use
Comodo Internet Security, it's free and it works very well for me. The firewall is great and the AV is much better now than just a few years ago. Just remember to pay attention to what you select during install, and disable that sandbox when finished if you don't need it.
On a new computer with Windows preloaded, reinstall it the first thing you do. On a friends HP Atom netbook, 55 GB was already used, that's just hilarious.
If you don't know how to do it,
follow this guide, it works with any brand.
I know that the recovery discs you make with Asus actually gives you a clean install (about 45 processes), the same for HP if you choose "Minimal installation", at least that's my experience. Sony discs won't do any good in this regard, you end up with 90 processes, nice.