There are various steps one can follow to fine-tune server performance, depending on skill level and the kind of control one has over the webserver. The following are topics which may be of useful consideration especially if your server is performing poorly.

Operating System

The general rule is that Linux-based webservers are easiest to tweak for optimal performance and provide easier use for most people running websites. For some there may be a slight learning curve, but this is easily overcome.
Using Windows-based servers is more complicated especially due to security weaknesses, more complicated requirements for setting file permissions, and harder-to-configure services. Naturally an MS fan may feel differently, but most web professionals will agree that Linux is the better hosting platform, unless a rare situation occurs where the website is dependent on very specific services only offered on a Windows platform.

Webserver Engine Software

For optimum security support, Zen Cart recommends using Apache as the webserver engine.

Apache

With Zen Cart, Apache v2 is required.
Apache must have AllowOverride set to 'All" or "Limit Indexes Options".
Without this you will receive errors due to the use of .htaccess security protections which prevent abuse of your server by hackers and which prevent phishing scams from being set up inside your site.  "Internal Server Error" messages will appear if AllowOverride doesn't support these.

IIS

If you are unfortunate enough to be hosted on a Windows server which runs IIS instead of Apache, you will not be able to benefit from the .htaccess security protections. In this case you will need to work with your hosting company to recreate those protections another way within IIS. Many of them will not even be possible to replicate.

Alternative Webserver Engines

If you don't use Apache or IIS, you will have to alter the .htaccess directives to suit your webserver's requirements. In many cases the intended protections cannot be recreated for other platforms.

PHP parameters

- memory_limit should be set to 16M or higher for basic use on a simple small store.  32M or 64M recommended on sites with larger numbers of products or many addons
- max_execution_time is commonly set to 60 seconds, which should be fine
- max_input_time is commonly set to 60 seconds, which is normally fine, except if you're doing large uploads such as huge photos or large input files with addons like ezpopulate
- file_uploads must be set to "On" if you expect to be able to upload files either via your admin interface or receive files from your customers
- post_max_size should be set to 32M or larger if you're uploading large images or large attachments/imports
- upload_max_filesize should be set to the same as post_max_size
- CURL must be compiled into PHP with OpenSSL support selected
- gzip compression should be enabled: zlib extension should be loaded and zlib.output_compression should be set to a non-zero value

MySQL Tuning

In MySQL, the server's my.cnf file contains the configuration settings for the database engine operation.  The default settings are typically inadequate for optimal use, and thus require tuning for your database to run smoothly.

Tuning MySQL is a carefully-guarded skill by industry professionals, since the knowledge is specialized and the expertise of professionals skilled in this topic commands a high price because it typically affords the benefactor a competitive edge.

Here are some tips with which you can experiment if you have control over the MySQL configuration (most storeowners will not have this level of access, and must rely on their hosting company's server administrator to do this sort of tweaking because it affects EVERYONE running on that server).

Server RAM

Note that the more RAM you have available to MySQL, the more room you have to play when tweaking. It's important to give a careful balance between MySQL and other services.

Memory Model

You need to increase the memory allocations beyond the standard settings. If you don't declare the sizing in your my.cnf it will use wimpy defaults which are generally inadequate.

The sum of all read/sort/join buffer size settings, and total tmp tables multiplied by tmp table sizes, and cache size settings plus memory per connection multiplied by max number of connections should be no more than 90% of available memory allocated to MySQL

Caching

table_cache should be large enough to handle the number of open_tables at any given time, plus 5-10% room to spare
table_definition_cache should be set similarly

thread_cache_size needs to be large enough to support the number of threads_created and threads_cached per second

Buffers

key_buffer size should be set to a level which suits the amount of index usage occurring on your server. Using 15-20% of system memory is common. But if this value is too large you're wasting resources that could be used better elsewhere.

read_buffer_size should be under 8M, and usually more than 2M. Increase it depending on the number of table_scans happening on an ongoing basis.

read_rnd_buffer_size might benefit from being 2M or larger

join_buffer_size and sort_buffer_size often do well at 1M but sometimes increasing this to 2M may be beneficial

tmp_table_size needs to be large enough to handle the memory demands of any temporary-tables created by query joins. Poorly written joins on improperly indexed tables will create higher demands on this setting

Connections

max_connections vs max_used_connections -- Don't set max_connections way too high, else you're wasting resources. Your max_used_connections should be more than 10% of your max_connections.

max_open_files vs open_files -- you should be using less than 75% of your max_open_files setting

Processes

You'll need to refine the number of child processes to be spawned before they are killed by the server. You do NOT want to have excess numbers of idle processes in MySQL, as this wastes resources. This is a combination of max_connections and connect_timeout, wait_timeout, max_connect_errors

Slow Query Log

It may be useful to set log-slow-queries so that someone skilled in understanding the logs and altering queries for performance can review them for tweaking.
Setting long_query_time to a value small enough to catch slow-running queries will help. This number may need adjusting over time. 2 might be a good starting value.
Be aware that this log can grow VERY large very quickly if there are many problems and slow queries. Beware.

General Advice

Use your favorite search engine and look for articles on mysql tweaking or optimization.

You will find much on the subject and it is really a balancing act. Determine what works best for you.