Well this question is old, but still relevant anyway.
Of course, it depends on your applications and requirements, but since you'd already be doing much more than just managing storage, the second option might be the easier choice. Why install a separate FreeNAS vm, since you'd be using a full-blown Linux distribution anyway? You wouldn't have the fancy FreeNAS web gui (unless you copy that manually), but that's usually not that important (there's nothing the web gui can do that you couldn't do manually).
Other than the web gui, the operating system kernel is a major difference, because FreeNAS uses FreeBSD, which (unlike Linux) has had ZFS included in the kernel for years. Of course, there are many other differences between those systems, but storage-wise, ZFS is probably the most important one. For Linux, there is ZFSonLinux (ZoL), which is actually pretty rock-solid. And support is excellent, just join #zfsonlinux or open a bug on Github if you've found a problem.
So, for those who have similar requirements, simply installing a minimal Debian or Fedora system might be the easiest way to go. ZoL has an official Debian repository, so installing ZoL is just a matter of adding the repository and then installing ZoL like any other package. Same for Fedora. On other distributions, it might be necessary to rebuild the ZoL modules manually (on every update), but that could be automated.
Once you have your minimal system, you can go ahead and install Apache, Git, Samba and all those nice things. This is also where it makes a difference what distribution you choose, depending on your requirements. If you want a stable system and don't have a requirement to always use the latest version of every program, Debian might be a good choice. The software in the Debian repositories is often rather old but if it works for you, that's all that counts. And you can stick with one Debian release for years (at some point, you will have to upgrade, but again, we're talking years). On the other hand, if you need to use the latest version of whatever software you are using, Fedora might be a better choice. Software available in the Fedora repository is usually up to date. A storage-related example where this makes a difference might be btrfs, which is an alternative to ZFS as it offers similar features (checksum data integrity, snapshots, cow, raid, ...) but it's part of the Linux kernel. The core functionality of btrfs is actually very solid as of today (July 2015), but you really should stick to the latest version because bugs are fixed and features are improved all the time. Fedora 22 currently ships with Linux 4.0, while Debian 7 comes with 3.2, which is really old (btrfs wasn't as stable back then, many significant bugs have been fixed since then). Even Debian 8 comes with 3.16, which is fairly recent, but still too old for btrfs (especially since there have been very important feature updates in 3.19). A drawback of using Fedora might be the release cycle, you'd probably have to upgrade about once a year. Then again, upgrading Fedora is really easy and usually hassle-free compared to other distributions.
Another point, since this is about the HP MicroServer: You're not limited to the 4 hdd slots for storage. First of all, you might want to install the operating system on some USB thumbdrive to not waste one drive for that. This server has a USB connector on the mainboard. Furthermore, some people have installed a 5th drive slot in the 5.25" front bay. If even more storage is required, a SAS hba could be installed and one or two (or even many more, chained, using expanders) drive enclosures can be attached. One MicroServer could manage tens of zpools (or btrfs raid volumes) with hundreds of drives, theoretically.
For more information on the hardware, see http://n40l.wikia.com/wiki/HP_MicroServer_N40L_Wiki.