Server with 3 Disk, what's the best HD Configuration?

Best option is to buy a 4th disk and R10 them.

RAID5 can be a little dangerous if you do not have a hot spare. If one drive fails, you'll need to replace it quickly, so that you don't risk a double-drive failure. Also during the failure, a RAID5 array will be noticeably slower.

I like to do RAID1 + 1 hot spare, which usually does well for mid and low-range servers (web servers, app servers, small MySQL database servers).

If your hardware RAID controller supports something like what IBM call RAID1E (Linux can do something similar with its software RAID10 driver in 3-device mode, Windows to me knowledge can not, support on hardware RAID solutions will vary) then that may be the most efficient solution.

Such an arrangement tends to read like RAID0 (must as RAID5 does) but has write performance metrics more like those of RAID1 (unlike RAID5, which can be much much slower for some I/O patterns), gives you the same redundancy of RAID5 (any one device can be in a failed state at any time and the array will recover once the bad device is replaced) and the same usable storage size (twice the size of the smallest drive).

If you are particularly worried about redundancy and potential downtime, then a three-drive RAID1 may be better. This costs space (only getting one drive's worth) but improves resiliency as any two drives can be in a failed state and the array still be fully operational. A good RAID controller will give you a read speed bonus for many load patterns too. If both are supported then I would recommend a three drive RAID1 in place of a two-drive array with a hot-spare because you do not have to wait for the array to rebuild onto the spare when one of the main drives dies and you don't have the risk of the spare failing to spin up when called into action due to not having been used in the X months/years since it was installed. Most if the time single-failed-drive protection is sufficient as double failures are much more rare (except in extreme cases, like a controller failure or power surge that gets as far as the drives, that might well take all the drives out at the same time anyway) and that sort of occurrence is what you network-local online backups are for.

RAID 5 will give you more space, but it will be slower; you'll also need to buy a new disk ASAP, should one of you disks fail, both for safety and because RAID 5 will become dramatically slower if one disk fails.

RAID 1 with a hot spare will be faster and more secure, but you'll end up using only 1/3 of your available disk space, which can seem quite a waste.

I'd not, anyway, go for any configuration without RAID; that's just asking for troubles.

If you can afford buying another disk (which you should, anyway, if you plan to use RAID 5), then a single raid 10 array or two RAID 1 ones would be your best option.

I would consider no raid with some sort of online data protection (such as Carbonite). This will maximize disk (750MB, say 600MB for data). Perhaps you split the drives into 3 250MB volumes and put data on two of them and the OS on the third.

Stefan's suggestion (RAID1 2 disks,l have a hot spare) is the safest, but only nets 250MB total disk. If you can make do with that little space, I would also recommend it.

Your second idea (1 drive unprotected for OS, RAID1 2 drives) nets 500MB, but only 250MB for data. I don't have a huge problem with leaving the OS unprotected as long as you backup your configurations to the protected drive, but I don't see it buying you much over 2 x RAID5 plus a hot spare.

Your first idea (RAID5 3 disks) is a compromise. You get more data space (400MB), but most experts advise against installing the OS on a RAID5 volume. If you do this, I strongly suggest purchasing a spare and having it handy so that you can swap quickly.

Finally, what I would really do if possible is get 2 small, fast drives, mirror them for the OS, then RAID5 the 3 500MB drives for the data, something like this answer to a similar question.