I don't think the 5900 RPM HD will make such a great performance difference versus a 7200 RPM version, in particular in combination with a SSD. As long as you split the usage between the SSD and HD in a way where you can utilize the speed of the SSD.
The SSD gives a tremendous performance boost when loading applications. If you have enough spare RAM you could use it easily as RAM disk for compilation work or any temporary data storage.
I wouldn't use the SSD for data storage with lots of writes as todays SSDs give you only 3000 writes per memory unit. If you do plan to use the SSD for heavy write access you should leave plenty of SSD space spare.
At the price of your SSD, you could also consider a second SSD later on if you see your SSD fills up and you do have many writes. Reading doesn't have an impact on SSD life time so if you had a read-only file system it would last a long time.
I assume you are going to run Linux so pay attention to the partition theme. I'm using a 120GB SSD with Linux Mint on it and have the swap space on the HDD. In my case I have 32 GB of memory which gives me plenty of space for putting the tmpfs and other temporary file systems on RAM (for example /var/log, though you may want to have that on a permanent file system to check log files after a reboot).
If you're on Linux, I can also recommend using LVM2 or logical volumes.
Disk space is cheap these days and if you really need more performance of a HDD you can add another one and run it as RAID for performance improvement. Or use LVM in striped mode for better similar performance increase. Or even combine LVM and RAID.
I have 5 or 6 HDD in my old PC, from WD Black 250 GB 7200 RPM drives to WD 20 EARX drives holding 2 TB on 5600 (or 5900 ?) RPM disks. In this case the "slower" disks aren't any slower than the faster (7200 RPM) disks because of the higher density of the larger disks.
I would refrain from getting the latest 3 TB disks though, having read plenty of user reports about their troubles.
As for MySQL and database usage, I'm not an expert but I believe a RAID setup would improve data write and read speed, if that is not sufficient on your system.
Make sure you adjust the /etc/fstab file for your SSD drive/partitions to enable trim support on ext4 partitions (using "discard") and noatime to reduce the writes to your SSD (see
http://wiki.debian.org/SSDoptimization for an example).
Good luck!