Is there a transistor comparison chart or database to be found?
There are way too many transistor types, even if limited to bipolar as you seem to be asking about, for any kind of simple chart.  After a while you will converge on some favorite types for certain applications.  For example, my knee jerk small bipolar transistors are the 2N4401/4403 (in reality MMBT4401/4403, but the 2N numbers are shorter and easier to say).  Lots of people seem to like the 2N3906 or 2N2222A, but the '4401 is a bit more robust and still dirt cheap.

If you are new to this and are not looking for something out of the ordinary, go to a distributor site like Mouser and look around.  Lots of parts will meet the specs, but the price and quantity on hand will be good indicators of how mainstream it is.  This is a case where low price is good not only to save money, but a indicator of what volume the part is produced in.  The number of companies making basically the same part is another indicator.  Unless you have special requirements, don't get something special.

When I do have special requirements, for bipolar transistors I usually go to the Zetex (now On Semi?) site.  You will find much less overlap within any one manufacturer's line.  Most of them have pretty good selection guides that let you drill down to find the part that best fits your need.  However, the manufacturer won't give you much guidance on how obscure a part is.  If the manufacturer stocks and sells their own stuff, then this is less important.  If not, check a few mainstream distributors to see how popular and available the part is.  The less popular and available, the more you are putting future production at risk.

If you find yourself really needing a particular obscure part, the first thing you should do is go back to your circuit and see if a little rearranging can alleviate some of the requirements.  Sometimes you really need it, but you should ask yourself carefully why you need it if it looks like few others have needed it before.  If you still need the obscure part, look around at other manufacturers for other options.  Ideally you can spec two or three unique manufacturer parts for the specialized requirement.  That will give purchasing some options in a few years when one manufacturer discontinues your part.  In some cases it might mean putting two different footprints on a board so that different parts can be substituted depending on availability and price.  Don't be the engineer that painted the company into a corner.