Thanks guys!
Dave - what Allen said - pore fill some scrap of what you have first before deciding to use stain. Epoxy resin will darken the mahogany considerable and you may like that look.
Personally I hate covering up natural wood......... JUST KIDDING since I painted a top black and sunbursted another guitar.
But see Kim's thread about staining his Barbie pink mottled mahogany before you decide to do this. Sanding through the stain can get complicated during finishing. Also if you don't want the stain to look blotchy where end grain is present you have to dampen a cloth, dampen the end grain area, sand, repeat, several times to even out the stain job too.
I have stained a number of necks but try to avoid it by carefully matching neck woods to back and side woods.