I've most liked Frans Brüggen's various Haydn and Mozart recordings on Philips, his Rameau on Philips & Glossa, and his first Philips recordings of the Beethoven Symphonies 1-9, Schubert Symphonies 1-9, and the Mendelssohn 3-5 Symphonies. There's also a good Mendelssohn "A Midsummer Night's Dream". Other than those recordings, you might explore Brüggen's late live recordings of the Bach Mass in B minor, Bach St. John Passion, and Bach Easter Oratorio on Glossa, which I've preferred to his early Bach recordings on Philips.
--Haydn: Symphonies - Sturm und Drang, Paris & London - Orchestra of the Age of Enlightenment, Frans Brüggen
Bruggen's equally fine Mozart will probably have to be listened to on an individual basis, since to my knowledge it hasn't all been boxed yet. EDIT: I was wrong, there is an 11CD Box set devoted to Brüggen's Mozart for Philips:
--Mozart: Symphonies Nos. 31 & 35 - Orchestra of the 18th Century · Frans Brüggen
--Beethoven, Symphonies 1-9, Violin Concerto (with Thomas Zehetmair), Orchestra of the 18th Century, Frans Brüggen - I much prefer his earlier Philips cycle to the later live cycle from Rotterdam on Glossa,
--Schubert, Symphonies 1-9, Orchestra of the 18th Century, Frans Brüggen
--Mendelssohn, Symphonies Nos. 3, 4, & 5, The Hebrides, Orchestra of the 18th Century, Frans Brüggen
--Mendelssohn, A Midsummer Night's Dream, Orchestra of the 18th Century, Frans Bruggen
- YouTube
--Rameau: Les Boréades Suite; Dardanus Suite, Orchestra of the 18th Century, Frans Brüggen, Philips
Rameau: Suite Les Boréades, RCT 31 - 1. Ouverture
--Rameau: Orchestral Suites, Orchestra of the 18th century, Frans Brüggen, Glossa
Acante et Céphise (Orchestral Excerpts) : Ouverture
--Rameau: Suite "Castor et Pollux", Purcell 3 Fantasies, Orchestra of the 18th Century, Frans Brüggen
Purcell: Fantasia à 5 "Upon one note", Z. 745
--Bach, Mass in B minor, Cappella Amsterdam, Orchestra of the 18th Century, Frans Brggen, live in Warsaw, Glossa,
Mass in B Minor, BWV 232: Kyrie eleison (Chorus)
--Bach, Easter Oratorio, Capella Amsterdam, Orchestra of the 18th Century, Frans Brüggen, Pieter-Jan Belber,
Geist und Seele wird verwirret, BWV 35: Concerto
In addition to his well reviewed Beethoven Violin Concerto with violinist Thomas Zehetmair, already mentioned, Brüggen also recorded Mozart's Complete Violin Concertos & Sinfonia Concertante with Zehetmair and the Orchestra of the 18th Century, which is worth checking out (I liked these recordings),
Violin Concerto No. 1 in B-Flat Major, K. 207: I. Allegro moderato
As a soloist, I'm only aware of the recordings that Brüggen made on the recorder, as part of a group of pioneering musicians that included Leonhardt, the Kuijken brothers, Bylsma, Schröder, and others, in the early days of the period movement in the 1960s, when they were all driving around the Netherlands in a Volkswagen bus giving concerts.
--Italian Recorder Sonatas - Frans Brüggen, Anner Bylsma, Gustav Leonhardt, 1967:
- YouTube
--J. S. Bach: Flute Sonatas, etc.--Frans Brüggen, Gustav Leonhardt
Sonata in B Minor, BWV 1030: I. Andante (Instrumental)
--Handel Recorder Sonatas - Frans Brüggen, Anner Bylsma, Gustav Leonhardt, 1962
Recorder Sonata in A Minor, Op. 1 No. 4, HWV 362: I. Larghetto
--Telemann "Paris" Quartets - Frans Brüggen, Jaap Schröder, Anner Bylsma, Gustav Leonhardt
Nouveaux quatuors "Paris Quartets": No. 1 in D Major, TWV 43:D3: I. Prélude
Etc.
Hope that helps.