I guess there's nothing wrong with using a traditional LAMP stack, but I do hear that your resouces on a RPi are limited and such a system may have your RPi running sluggish. You'll need to check on the RPi forums about perfomance.
Another option, is to use a different commuincations protocol between your Arduino's and the GNU/linux system like RPi, such as using Modbus, rather than using HTTP.
Using Modbus then allows you to choose between using your USB or if you have already, Ethernet on both of your Arduino's.
Then, on your RPi or what ever you choose, you write a C program, much as you do in your Arduino, that uses a modbus library to then request the data you wish when you wish from any connected device, in your case, your two Arduino's.
So, rather than using a heavy bloated Apaché and PHP and MySQL install on a limited RPi, your C program talks to your Arduino's and then stores the data, say, either in text files or in SQLite database, to then do as you please.
Actually, this is the project I have been working on since April 2014, called QuadlogSCADA.
The current project I'm developing is specifically for small control monitoring systems similar to what you are wanting, but is designed to also fit into small industrial situations.
Quadlog operates on Intel32/86 and ARM based systems like Cubieboard and I guess RPi as well, where it uses Modbus to talk to devices like Arduino via USB/RS485 or Ethernet or actually to any device that talks Modbus.
The project also has an inbuilt HTTP server so you can then access any of your data, be it real time data or stored hstorical data.
The code is very lightweight and there is no need for any LAMP install base, just a few libraries used by the main application.
The project is still in early days, and is under active development and I would say is not quite ready for general use, but is being tested on a couple of sites presently.
Anyhow, if you wish, you can read more and see an example at my signature below, which itself is running on Quadlog at my location.