Know you not that around the animalcule that sports in the water there shines a halo, as around the star (The Monas mica, found in the purest pools, is encompassed with a halo. And this is frequent amongst many other species of animalcule.) that revolves in bright pastime through the space? True art finds beauty everywhere.--Zanoni, Edward Bulwer-Lytton (1842).
The classification of microscopic organisms long lagged behind that of other organisms in attention and reliability, for the simple reason that the technology to distinguish a significant amount of features in said microscopic organisms took a lot longer to develop. The really minute flagellates posed a particular challenge due to their particularly small size, as well as a shortage of distinguishing features between taxa. A review in the recent issue of Protist (Boenigk, 2008) looks at the history of classification of the nanoflagellates through the lense of the history of the first genus named, Monas Müller, 1773. Monas was long a receptacle for almost all minute flagellates (and even if not specifically referred to Monas, such organisms were still referred to as 'monads'), only to eventually slip into disuse as it became increasingly unclear what the name Monas had originally referred to (figure below from Boenigk, 2008).
When Monas was first named in 1773, life was still firmly divided between 'plants' and 'animals', and the concept of organisms falling outside these classes had not yet developed (Hogg proposed 'Protoctista' in 1860). The two kingdoms were distinguished by the motility of animals, making most protists such as Monas animals (and fungi into plants). It was only later that some protists were reclassified as plants due to their autotrophy (or more accurately, lack of particulate food uptake - fungi were still plants). Perty summed up the problem when establishing his order Phytozoidia in 1852 (as quoted in Boenigk, 2008):
Die zweite Ordnung [der Infusorien] kann den Namen Phytozoidia erhalten, weil unter ihnen sehr viele Formen sich befinden, welche in ihrem Lebenscyklus in Wahrheit bald dem Thier- bald dem Pflanzenreiche angehören, zwischen beiden oscilliren, während andere, bei denen dies nicht der Fall ist, so sehr in Gestalt, Bau, Bewegung und sonstigem Verhalten mit ihnen übereinstimmen, dass an eine völlige Trennung nicht zu denken ist.
[The second order [of the Infusoria] may get the name Phytozoidia as it contains many forms, which in their life cycle truly belong at times to the animal — at times to the plant kingdom; they either oscillate between both, or, when this is not the case, are that similar to the former in shape, structure, motion, and other behavior, that they cannot be separated.]
The genus Monas was first established with three species, M. termo, M. lens and M. mica. Monas termo has since been reclassified to the chrysophyte genus Oikomonas while M. lens is now in the kinetoplastid genus Bodo, leaving M. mica as the effective type species of Monas* (Silva, 1960). Over the years, more than 100 species have been assigned to Monas with little more to unite them than being small, fairly nondescript and (usually) with flagella. Different authors have applied different definitions of the genus, often in complete contradiction to each other (for instance, Bory  defined Monas as lacking caudiform appendages, while Dujardin  defined it as possessing a single flagellum). As recounted by Boenigk, species attributed to Monas eventually turned out to belong to the entire range of protist groups - amoebozoans, fungi, chlorophytes, excavates, even a few bacteria.
*As with many if not most protists, it is a little unclear whether Monas should be treated as a name under the Zoological or Botanical Code. The typification of the genus by M. mica through removing the other two species is valid under the ICBN, but not necessarily so under the ICZN. Nevertheless, we'll accept M. mica as the type species of Monas because there's no reason to unnecessarily tick off the botanists.
So what does the name Monas ultimately belong to? Unfortunately, that's where we must draw a blank. Boenigk (2008) gives us the original description of Monas mica (as well as the original illustration, shown above):
Lenticula 3. microsc. simplicis puctulum lucidem conspicitur, aucta vero magnitudine animalculum ovale vel sphaericum, nam utramque figuram pro lubitu assumit, exhibetur. Hyalina est, circulo ovali intus inscripta; hic mobilis est, & in medio, vel versus antica vel versus postica videtur. Motus vacillatorius; saepe eodem in loco, assumata figura sphaerica, diu gyratur, tumque impressio reniformis oculo in medio corporis sistitur, animalculumque halone, absque dubio e ciliis vibrantibus invisibilibus orto, pulchre cingitur. In aquis purioribus passim.
[Under the lens 3 of a simple microscope it is seen as a bright dot, yet at higher magnification as oval or spherical animalcule, because it adopts at times the one, and at times the other shape. It is hyaline, with an oval shape inside, here it is motile and seen either in the centre or anteriorly or posteriorly. With trembling movement; often rotating in one place, then with a spherical shape but with a persisting kidney shaped depression near the centre of the body, and the animalcule is surrounded by a nice halo, which arises without doubt from trembling invisible cilia. In pure water.]
There's only a few thousand taxa to which that description could apply to choose between. In fact, the description is a little vague as to whether the organism in question was even a flagellate - the presence of flagella was only inferred from the 'halo', not demonstrated. Later descriptions of Monas mica in Pritchard (1834) and Hogg (1854) add little to the original description, though both repeat the description of a halo, as for that matter does the passage quoted at the top of this post*.
*Edward Bulwer-Lytton was an immensely popular Victorian author whom Mary Shelley described as the "first author of the age". Modern audiences have a slightly different opinion of him - San Jose University in California established its Bulwer-Lytton Fiction Contest for the worst beginning to an imaginary novel in memory of the opening words of Bulwer-Lytton's Paul Clifford - "It was a dark and stormy night...".
A general assumption has evolved that Monas is vaguely equivalent to the chrysophyte genus Spumella. However, Silva (1960) demonstrated that this association was not connected with any of the original species of Monas, but due to the species described as M. vivipara (now Spumella vivipara) by Ehrenberg in 1835. As a result, there is no reason to associate Monas with Spumella any more than with any other flagellate genus, and the suggestion by Cavalier-Smith & Chao (2006) that Monas could be used for one of the clades of the also polyphyletic Spumella lacks any taxonomic justification. Despite having a long and exalted history, the name Monas has fallen into obscurity, and there it must stay.
Boenigk, J. 2008. The past and present classification problem with nanoflagellates exemplified by the genus Monas. Protist 159: 319-337.
Cavalier-Smith, T., & E. E.-Y. Chao. 2006. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). Journal of Molecular Evolution 62 (4): 388-420.
Hogg, J. 1854. The Microscope: its history, construction, and applications. Being a familiar introduction to the use of the instrument and the study of microscopical science. The Illustrated London Library.
Pritchard, A. 1834. The Natural History of Animalcules: containing descriptions of all the known species of Infusoria; with instructions for procuring and viewing them, &c. &c. &c. Whittaker and Co.: London.
Silva, P. C. 1960. Remarks on algal nomenclature. III. Taxon 9 (1): 18-25.