I currently run gentoo on my laptop, and ubuntu on my desktop. I already have lots of experience regarding linux. In a few weeks, Ill be entering university.
Although I find that gentoo is one of the awesomeest distros ever, I have to admit that it requires more maintenance and work than other distros. However, I absolutely adore the fact that I can get the newest software, and that it has high stability. Much of the stuff on my system, like mesa gallium (svn) is only available from gentoo. Only mesa from svn performs well on my laptop (ati mobility 3650). This applies to other libraries and programs as well.
In the end, however, with using gentoo, I lose a lot of compatability, due to the fact that Ubuntu is quite popular. Most devs will package their programs for Ubuntu, or in a RPM. I know that I could simply install the deb/rpm, but a lot of times, it simply doesn't work (adobe air anyone?). Even if they support Ubuntu at the university (UoT), I likely won't be included in the circle of support.
Even though I started off in Linux with Ubuntu, I haven't used it much over the years as I converted to gentoo.
Would it make sense to install gentoo on the desktop instead, then install windows 7 (need it for classes) and Ubuntu onto the laptop (which im brining to university)? or to keep the current setup?
Whichever you might like to use. Ubuntu is pretty vastly used other than other distro so that's why most spotlight goes to Ubuntu instead of Gentoo.
I don't see a hassle working with Gentoo if you already know how to use it more than Ubuntu but then again Ubuntu has less maintenance which is good for portable purpose. So I think you should go just like you suggested
Gentoo for desktop dual-boot with windows (xp/vista/7)
Ubuntu for laptop (also can dual-boot)
if you have lots of free space to use on either desktop or laptop, just install both Gentoo and Ubuntu together on different partition. Much like below
Primary Partition C: - ntfs - Windows
Extended Partition - ext3/4 - Gentoo
Partition - ext3/4 - Ubuntu
Primary Partition - ntfs - Available free space for storage/backup purpose
Here's a note to take before installing any OS's on your computer.
* Note that Windows can't detect ext3/4 partition format so they will be mark as unknown partition in windows. Linux distro on the other side can detect all partition type.
* You have to install Windows first before install Linux distro because of boot process. If you install windows last, you may not be able to boot to your linux OS's.
* Primary Partition can be created up to 4 partition only while extended can break those limit. Be sure to set one primary partition to extended to extend your partition number.