My favorite brand right now is U.S. Masters. The fit and finish are very much as "boutique" as Tom Anderson, Suhr, etc...These guitars are underrated beyond belief. The conical radius fretboard is so easy to play on. The compression set captive neck joint is another great feature and leaves very little neck heel. It's pretty much a similar thing to what the other boutique builders are doing. Very good stuff...
http://www.usmasters.com/highperformfeatures.htm
If you can find one on Ebay you can save some $$.
The other guitar I swear by is the Ibanez RG series. I have an RG3120 Prestige with Dimarzio pickups and it kills.
The radius is pretty flat though, so if you enjoy more of a traditional style Strat or Les Paul radius, it might not be your cup of tea. I agree with Drew. The RGT series is just awesome. Great for shred, but by no means a one trick pony. Plus, they just look hot. The only issue I have had is that the customer service is a little weak. Not horrible, but not great. Speaking of Ibanez quality...
My last suggestion is a little known guitar maker that has been quietly driving the industry for years. Ever hear of Bunker Guitars? Well if you have played an Ibanez made in the U.S.A. custom shop, it was built in the Bunker factory. Not a lot of Ibby lovers are hip to this:
http://davebunkerguitars.com/media_release.html
He makes some really killer stuff. I want to snatch up one of his Strat clones. He does it semi custom where you can choose options and upgrades to get you where you want. The best part is that right now they start at $599 factory direct!!! Seriously...That is just fucking amazing for an all US made rig. The technology behind the necks is very interesting and you can choose a variety of woods and options for a very reasonable upcharge. Gibson and others get their maple from Bunker as well. The patented tension free neck is fully guaranteed and warranted for life. Check em' out. As soon as I can afford it, I'm getting one in Tobacco sunburst with a flame maple neck and fretboard.
http://bunker-guitars.com/articles/guitars/classic-57.html
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