Here's a brief guide on troubleshooting graphics and stability issues in Saga, which I managed to dig up from 2008 - hopefully most of it is still relevant:
Firstly, it's a good idea to run a defrag after a new Saga patch is released. This gets all of the Saga files together in one location on your hard drive for better performance and stability. Third-party defragmenters are available for free, such is this one: http://www.piriform.com/defraggler/download
Next, make sure you've got the latest drivers for your graphics card. If you're unsure which graphics card you've got, this free utility can find out for you: http://www.techpowerup.com/downloads/SysInfo/GPU-Z/
If you have an ATi card: http://support.amd.com/us/gpudownload/Pages/index.aspx
If you have an nVidia card: http://www.nvidia.com/Download/index.aspx
When upgrading to new graphics drivers, it's extremely important to completely uninstall your old graphics drivers first! Installing new graphics drivers over the top of old graphics drivers often causes glitches, weird artifacts, and other undesirable effects. (Update: I believe drivers in recent years automagically uninstall your older drivers for you during the installation process.)
Next, go into your graphics control panel in your computer. Ensure that your graphics settings for gaming and 3D applications has everything set to "application controlled" that you can set as application controlled. This is important, as some new graphics chipsets are capable of some settings that Saga and other applications are not capable of. Trying to force applications to use some of these advanced settings will result in undesirable effects. Thankfully, the default settings for most graphics drivers have things set at application controlled.
Now for Saga itself! Click on Options from the yellow banner up in the top right corner in your Saga game. Unchecking Trilinear Filtering often will reduce lag. Setting Anti Aliasing at 1x and Texture Filtering at 1x will improve performance, although 2x on each is a good balance between quality and performance. Tree Density, Grass Density, and Grass Distance can all be turned completely to the left to improve performance, if desired. (This also takes care of pesky trees which might obstruct your view.) If you often have problems where you log into your city and see nothing but water, uncheck the box for Dynamic Lighting.
Also in the Options menu, click on General. If you've got a multi-core CPU, check the box for Multithreaded to improve overall game performance. To make your city look pretty with more building animation, check the box for Building Particles.
Now click on the yellow Social banner. Chat can cause some lag, so click on the options tab. This gives you the ability to configure the various chat channels. Clear all checkmarks from tabs 2, 3, and 4. Have all boxes checked for tab 1; and have only General, Guild, and Whisper enabled for Battle. Whenever you experience lag in Saga, you can also type the "/clear" command in the chat box to clear your chat history and free up some RAM.
Hopefully this guide is helpful to you all!