I have both the 6000L and the 1000, so I'll chime in with my 2 cents...
First off, the keyboard on the 6000 is the biggest gripe for me, as compared to the 1000 keyboard. This is a matter of personal preference, but I just can't type efficiently with the 6000 keyboard because of the overall layout (no seperate row for numbers, etc.). I just seem like I have to use two keys to get the number/character that I need more than with the 1000.
I have an ambicom wifi card and it is almost always inserted into my 1000, unless I'm trying to conserve the battery. Even when I'm not using the wifi to browse the web or whatever, I still keep the card in when using the keyboard. The card sticking out just doesn't bother me at all.
I also prefer the landscape screen for most uses. Also, the clamshell design is great for super lazy people like me. For instance, I like to lay down in my recliner and put my 1000 on my chest with the screen angled perfect for reading. Then I set opie reader on auto scroll, and I'm set for hours without lifting a finger!
Now, the thing that I love most about the 6000 is the built in speaker and mic strategically placed to be used as a VOIP phone on the back. I don't know why, but I just love using my 6000 as a phone.
The built in wifi on the 6000 is nice too, but I'm so used to having my cf wifi card with my z at all times, it's just second nature now.
Good luck!