Yngwie's Ultimate Weapon
Yngwie and the Fender Stratocaster are about as synonymous as you can get in terms of an artists allegiance to one particular instrument.  Yngwie has collection of Stratocasters that totals over 200 with models ranging from early 1950's model to present day Custom Shop instruments. 

Yngwie's favoured period of Stratocasters are those built between 1968 and 1972 and particularly those in a Vintage White colour.  Perhaps Yngwie's best known Strat is a 1971 model nicknamed 'The Duck' (due to a Donald Duck sticker on the headstock).  This is the same guitar seen on the cover of the "Rising Force" album.

Yngwie is quite unique in the heavy metal field to be playing a Stratocaster.  The pairing of guitar and amplifier (see amp section) is quite important as a Strat with a modern hi-gain amp can often sound thin or buzzy.  Yet due to Yngwie's penchant for vintage 50 watt non master volume Marshall's this (coupled with an overdrive box) leads to a very full rich sound which superb clarity and note definition. 

If you are chasing the Yngwie's tone and have a Strat don't pile on the preamp gain, you are aiming for a clear tone - listen to how clean the Yngwie tone actually is on. A lot of Yngwie's tone is in his hands - the fluidity, the sustain, the pairing of Stratocaster and vintage Marshall is a setup that will highlight any flaws in your playing.  But will reward with superb tone if you work at it.

Scalloped Fingerboard - Scalloped fingerboards are carved between the frets to create a playing surface where only the strings themselves are contacted by the players fingers. The players fingers never touch the fingerboard. This offers advantages to the experienced virtuosos: The player experiences drastically reduced friction during string bending and vibrato, and therefore has the potential of increased command of the strings.
Dunlop 6000 frets - Super Jumbo fret wire #6000 replaces all Fender std frets.

DiMarzio Pickups  - "HS-3"  in the bridge position /  "YJM" in the neck and middle position.  
These pickups were designed in conjunction with Yngwie.  New users may initially be shocked by the relatively low output of these pickups in comparison to stock Fender single coils.  The reasoning behind this is to get a clear a signal as possible from guitar to amp and this is where the DOD YJM308 works its magic (see amps and effects page).

Brass Nut - adds a little more presence to open chords and open strings. See in the left picture above.

Disconnected both tone controls - give a little less impendence allowing a little more output from the volume control..

3 bolt Strat neckplates upgraded to 4 bolt (for live instruments) - improved neck stability and sustain.

These modifications (apart from the disconnected tone controls) come as standard on the Fender Yngwie Malmsteen Signature Stratocaster.  However, any good Strat will give a YJM-ish tone.  Remember, Yngwie has always tended to favour vintage instruments over Signature guitars.