I am trying to build a database server that's going to have to be on 24/7 in my bedroom, and am trying to make it as silent as possible within my budget.

I am thinking of using one of the new 65W i5's with a Tower Heatsink, and relying on a 120mm exhaust fan to keep it cool. Based on experience I think this will work, especially since I'll be using the i5's integrated graphics and won't have to deal with the heat from a Video Card.

The thing is, this is going to require some sort of Tower heatsink, and I have no clue what sort of Tower heatsink (if any) will fit into a micro-atx case?

Anyone else go down this route and have advice, or specific models?

What specific case do you have in mind ?

As already said by frenchie, it depends of the mATX case. Do you want a really small one?

However, in an enclosure such as the venerable Antec NSK3480 (or as the Silverstone TJ08/TJ08-E) almost anything should fit (anything less tall than a Thermalright Archon, or less wide than a Scythe Susanoo, I mean).

One of the most recent 3480 in the SPCR gallery.

However, if I may take the liberty, I mean that you may not need such a solution for a database server.

IMHO even a smaller heatsink, like the Scythe Big Shuriken, might suffice more than enough, without any noticeable trade off with reference to quietness or cpu temps (I have a MS SQL system - but mostly for development - running on a 3.0GHz quad core AMD with that heatsink).
Then, even the enclosure might be smaller (as the quoted NSK3480 is a compact case, but it's not one of the smallest).