You can do very well with Bacula/Amanda. Hitting your requirements:
Revisions (SVN-style): a file has to be backed up each time it gets modified (and multiples versions of the same file can exist on the server, in fact they must)
Bacula and Amanda will grab a file each time it changes.
Scalability: if I attach an USB drive to the computer, I want it's data to be backed up as well (well... That on linux might be quite easy, simply backup all /media/ except cds and dvds, but for windows?)
Not bad on Unix (Just back up everything under / and it will grab the media), but probably not possible on Windows -- I believe you need to specify the drives you want to grab because the filesystem isn't a tree hierarchy under a specific root (there's a root for each drive).
That said, it's probably NOT a good idea (What if you attach a full 1TB drive to a machine being backed up? Your backups just ballooned).
Near real-time (~ 5 minutes at max) file backup: I lost a latex report and was hard to reconstruct it from scratch
Not happening -- You CAN specify a 5 minute backup window, but your logs will be filled with jobs being killed because there's already a duplicate running.
You can schedule nightly backups, or even every 12 hours without much trouble.
(Even Apple's Time Machine only does hourly backups... think about the largest file that may change and have to be shoved over the wire...)
No-Duplication: for instance if I backup the USB's disk content from 2 different computers, I do not want the data to be backed up twice (symlink instead of hard copy in worst case)
Bacula doesn't have deduplication at this time. Not sure about Amanda.
Manual restore / automatic restore: it's the same for me (simply not like described here below)
Restores are (and should be) a manual process. I have no idea what an "automatic restore" would look like (the backup server decides on its own to restore a file? :)
Maybe ability to remove / exclude large files from backups
You can include or exclude specific parts of the filesystem (down to file-level granularity) in Bacula.
Good logs
Database-backed lists of jobs and results, with the ability to write to log files, email, etc. in the event of errors.
BackupPC may also be able to hit these requirements (not certain - haven't used it) - other commercial backup solutions almost certainly can as well.
You may also want to consider tarsnap, though I'm not sure how the Windows support is.
I have always had much better success booting the physical system with "Parted Magic" USB or CD, imaging the system with Clonezilla (from inside of PMagic), then restoring in the virtual machine with the same Parted Magic disk.
If you are migrating a Windows machine, "mergeide" might also be quite helpful for you.
More on mergeide: http://www.biermann.org/philipp/STOP_0x0000007B/
Best Answer
In my experience, building a PC/File Server from scratch doesn't come close in terms of power efficiency to most consumer level NAS devices. With that being said, full-blown computers are obviously much more flexible/capable then consumer NASes, however home built anything will always consume more electricity. If you're lucky, you may be able to get consumption to within a few watts to consumer-ish hardware, but the time/effort/money may not be worth it.
I have NAS at home hooked up to a UPS, and just with the simple UPS monitor, it ranges from 45W-55W with just two drives. During off-peak times, it can get into the 30w-40w range. I have seen it as low as 25w but that's not common. That's not too shabby. Granted I have a 4-disk NAS, it's easier to operate, small and very energy efficient. Building is always fun but in the end can cost more, have more problems/maintenance, is physically much larger and consumes more electricity than a consumer-NAS counterpart.
It's kind of odd that redundancy isn't a must considering it's a file server, but to each his/her own. If cost is the biggest issue and speed/redundancy are supplemental, 2-drive NAS devices should suffice.
Off the top of my head, I'd recommend the Netgear ReadyNAS Duo RND2000. It retails around $300+, but look on online retailers and you'll see they sell it for less. I think there's also a big rebate from Netgear on it as well these days but I'm not too sure. Note, Netgear sells most of their NASes with hard drives so prices seem to be inflated. Make sure to search for diskless versions.
Another NAS I'd recommend is the the QNAP TS-239 Pro. I own a TS-409 Pro but I've been very happy with QNAP as it's pretty rock solid. The software it comes with is fairly easy to use and works reliably. It's running Linux embedded so if you really want to dig into the internals, ssh access is available.
2 Disk NASes are fairly economical. The price range is fairly small from $100 to $300. 4 Disc NASes have a wider range of prices that will probably discourage you. They can range from $500-$900+. But it sounds like money is an issue so I'd go with 2-disk in your situation.
I would stay away from this idea. While it may be the most economical/hacker-ish type solution, to me it smells like more trouble than it's worth. I've used DDWRT and Tomato and they're both fine ROMs for wireless routers/firewalls/vpns but file serving isn't something that I saw as a major priority with both projects. I could be wrong these days as it's been a while since I've used/played around with both, but if your files mean anything to you just get a cheap NAS device, hook it up to your LAN and call it a night.