I am aware that removing applications when you are rooted may cause you to brick or run into issues when installing froyo, but can you also run into issues installing root applications such as droidcap?
Basically: If I root to install DroidCap could I safely upgrade to 2.2 in the future and not worry about unrooting?
Root-only applications can be removed as well as root so you'll be able to upgrade fine.
Technically, you'd be fine to remove any bloatware that you wanted but in order to update, you'd have to reinstall them and then go in and change the properties to match those of "system applications" but that is a PITA, trust me, I already had to do it. Lesson learned for me. I'm not removing any bloatware for a little while now.
Also, if it's really bugging you too much, you can always just rename the boatware files from insertapplicationnamehere.apk to insertapplicationnamehere.apk.old.