There are a few meanings. If you haven't heard it before, I am guessing you hear it in a context like "the LAMP stack." Basically, web applications are complex systems these days, and they rely on moving parts on top of moving parts. Stack describes that collection of programs/technologies.
For example, Bingo Card Creator uses a fairly typical Rails stack: application code in Rails(a web framework based on the language Ruby), MySQL for the DB, Nginx proxying to mongrel for the web tier, memcached and Redis for for a few purposes, DelayedJob for queuing, all running on Ubuntu.
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In short: a data structure where the last thing you put in is the first you get out.
To others it means everything you can pile up in one or the other way. Like MySql on Linux with Apache and PHP which gives us the LAMP stack ...
To some weird people it might mean this: http://www.rocktownhall.com/blogs/media/blogs/rth/MarshallSt...