Which do you prefer? I like GPT because you get a lot of partitions.
And it's easy to conver to GPT

If you have to re do your partition layout it's best just to switch to GPT. When you eventually upgrade to that new system then everything will be good to go... Unless for some reason you need to view that hard drive from a system that won't understand GPT.

I actually switched back to MBR because I only use 1 distro and for compatibility reasons

I use MBR as well.

BTW do some linux distros have trouble understanding GPT partitions as stated by the compatibility issues?

I use MBR. I don't need something else, so if it works don't fix it.

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Not sure when the support was added but any recent GNU/Linux distro should support it. If you need to use Windows XP or earlier to access any of the partitions on the disk, then you need to stick with MBR. I don't know about Vista, but Win7 supports GPT.

One note however. If you are using a system with a bios, you need a special 2mb MBR boot partition and a MBR armored GPT table. That allows the bios to load the boot loader which then loads the initrd image that understands the GPT. This is the default in Fedora 16 when installing from scratch.

Also, you are better off using Grub2. Grub1 has no official support for GPT. 'lilo' should theoretically work, but I didn't want to tempt it.

And my statement was geared towards somebody who plans on upgrading eventually and just wants to toss the old hard drive onto the new system and want it to work.... Maybe I'm wrong on all of this, I only switched to GPT because I wanted to play with it and see if I could.

MBR.

Since I beta-test software across multiple platforms, I need all underlying systems to be current and stable to eliminate possible compatibility issues.

LILO worked when I used it with GPT

Why 'lilo' and not lilo? It does work and I can confirm it. One of my computers has a gpt partition table. I did it because I wanted to install OS X to see what all the hype was about - average system at best.

Why not LILO? Probably the way I typed it. I grew up (linux wise) on Slackware so I quite like lilo. Simple, to the point, stable, supported all the latest file systems and what not before Grub and Grub2. For now, I'm on Arch and tried out Grub2 with GPT, 2MB protected MBR, root fs with LUKS Encrypted BtrFS. No complaints for now.