This might seem like a silly question, but what's the difference? What's wrong with using an app? There are tons of notepad apps for free in the market and it takes 30 seconds to get one.
You know, before I got the phone, that question never entered my mind. I kinda assumed that it was a standard (me being jaded with my iPod touch). But, it kinda doesn't make sense that there would not be a stock note taking application. At least a very basic one.
So, well, to answer your question, no, there isn't a notepad app. But to be honest, I would likely ditch the preinstalled one for an app called Evernote. Coupled with the desktop client, you can automatically sync notes onto your computer. Rather than emailing it to yourself.It can also do audio and pictures as well. You can see what you get for the free version here. I have been perfectly happy with not having their Premium service.
I can understand that. I'm like that too. Well, I guess it doesn't have a notepad, but it's really no big deal. You'll probably like one of the free notepads on the market much more than you WOULD have liked any ol' stock notepad. Hey, the apps are free so why not use 'em?
One other note: when downloading apps from the market be sure to pay attention to the privileges that are requested. If the notepad asks for access to your contacts and the internet, you might want to question why it needs those privileges. If there's a legitimate reason and from a seemingly trustworthy developer, then go for it. Otherwise, find an alternative.
Oh, one other stock app that I don't use much is the browser. I use Dolphin HD because you can set the user agent to desktop/computer. That way you don't have to just see mobile sites--you can view the real deal full web sites. Dolphin HD also has tabs. xScope is another good browser.