I don't think there is a single perfect protocol, because of the wide range of compounds of interest. There are so many types of compounds, with different chemistries and polarities. This means one single method won't work to isolate everything, so the initial isolation and screening is a matter of choice.

Most of us do some sort of screening. Since this post is under phytochemistry, I'll describe some methods for plants. Bacterial/fungal cultures are often done somewhat differently. Most of us will do an initial extraction with a moderate polarity solvent such as methanol or ethanol. Some people will extract their plant starting with hexane, then extract the same material in ethyl acetate, followed by dichloromethane, ethanol, and finally water. Others take the methanol or ethanol extract and dissolve the solid in those same solvents, the solid being mixed with the next higher polarity solvent. One then needs to determine the chromatography.

I like to do a "column screen". I run several types of columns (silica, alumina, diol, C18, SAX, and SCX) with the ethanol extract. This helps determine which columns might work, the compound polarity, suggest alternative chromatography solvents, and sometimes even suggest the purification procedure.

Here are some links: 

http://www.isco.com/WebProductFiles/Applications/101/Poster_and_Paper_Reprints/New_Techniques_In_Extraction_Column_Screening.pdf

Edit: I'll add the link for the ion exchange screening later. I wanted to upload the file but the researchgate uploader seems to be failing, either for chrome or internet explorer.

I don't think there is a single perfect protocol, because of the wide range of compounds of interest. There are so many types of compounds, with different chemistries and polarities. This means one single method won't work to isolate everything, so the initial isolation and screening is a matter of choice.

Most of us do some sort of screening. Since this post is under phytochemistry, I'll describe some methods for plants. Bacterial/fungal cultures are often done somewhat differently. Most of us will do an initial extraction with a moderate polarity solvent such as methanol or ethanol. Some people will extract their plant starting with hexane, then extract the same material in ethyl acetate, followed by dichloromethane, ethanol, and finally water. Others take the methanol or ethanol extract and dissolve the solid in those same solvents, the solid being mixed with the next higher polarity solvent. One then needs to determine the chromatography.

I like to do a "column screen". I run several types of columns (silica, alumina, diol, C18, SAX, and SCX) with the ethanol extract. This helps determine which columns might work, the compound polarity, suggest alternative chromatography solvents, and sometimes even suggest the purification procedure.

Here are some links: 

http://www.isco.com/WebProductFiles/Applications/101/Poster_and_Paper_Reprints/New_Techniques_In_Extraction_Column_Screening.pdf

Edit: I'll add the link for the ion exchange screening later. I wanted to upload the file but the researchgate uploader seems to be failing, either for chrome or internet explorer.

Nothing in this world is perfect.

Do literature searching and see what has worked for your organism in question.

Apparently no. And rightly said by Dr.Silver..

In my opinion, the answer is no, because phytochemistry work is totally a development method. It is not about perfect, but more about suitable for particular sample. Each sample is unique with its own chemistry and therefore, the way for scientists to isolate its chemical constituents may vary with others. There is no perfect kit in phytochemistry works.

I think question is not clear. which groups of compounds are being mentioned? All  must be based on a recovery test. Then you can say your protocol best or not prior to particular extraction. 

There is no specified protocol for isolation of secondary metabolites. It varies from one source material to other. You have to search for work carried out for your source material and accordingly move further for your interest of work.  

All respondents so far have precisely stated that there is no single standard protocol for isolation of wide range of secondary metabolites (SM) from various sources. Yes, methods for extraction, fractionation, chromatographic separation, estimation and identification are there and one has to choose and apply according the nature of work, source material and SM of interest.