Preference when using stains

Since I've become involved with ukulele building, I haven't done much research on staining up to now. On my first ukes I used Minwax oil based stains because I happened to have them lying around and was familiar with the results they produced. I didn't like the long drying time required, however and also was concerned about compatibility issues when used under lacquer. If left to dry long enough, this so far has not been a problem.
With my latest build, a teardrop soprano, nearing the finishing stage and coming along nicely, I thought it prudent that I should do more research and eventually ended up ordering ColorTone Liquid Stain sold by Stewmac. I was intrigued by the fact that it can be mixed with water, alcohol and lacquer.
I would be interested in hearing views on this, or other stains that you may prefer using. Is there a preference for one over another, or does it depend on the wood? So far, I have only stained mahogany darker because nearly all the ukes I've seen seem to be that way. Is clearcoating the natural mahogany wood acceptable?
I'd sure appreciate some words of wisdom from the wise on this subject to further my insatiable quest for knowledge!

Bob

Staining is a good way the get all the parts to match, since sides and backs aren't normally cut from the same flitch or board. A natural finish is dynamite if there is any figure or contrast in the wood, which tends to be hidden when stained. Mahogany is so often stained that most people don't recognize the natural color, especially if its a nice light brown.

Transtint, (same brand as Stewmac concentrate dyes)

Thanks for the replies, much appreciated. Beau, are you referring to Stewmac's stains, as I don't see concentrate dyes in their catalog. Or are stains and dyes the same thing in this category? Please excuse my ignorance

Bob

Transtint
http://www.woodcraft.com/search2/search.aspx?query=transtint

cheaper here
http://www.veneersupplies.com/categories/Veneering__Supplies/Veneer__Dye__&__Stains/

Stew mac (re branded Transtint)
http://www.stewmac.com/Materials_an...Tints_and_Stains/ColorTone_Liquid_Stains.html

Thanks again, Beau, for taking the time to reply. That's the stain I ordered, I guess I bought the right stuff!

Bob

for sun bursts, i use:
Tobacco brown (Mission brown in Transtint)
Vintage amber
Medium brown