Design for scientific data. Data table with hundreds of columns or data table with a generic value column and hundreds of rows (EAV)?
What you are describing is the EAV (Entity Attribute Value) model which most database professionals would run a mile from. It's also sarcastically called the OTLT (One True Lookup Table) and is a classic novice mistake. Your hunch is correct!

Here (and here) is the opinion of Joe Celko (a veteran SQL programmer who is/was a member of the SQL standards committee.  The fact that he titles his article with the phrase "EAV of destruction" should give you a clue :-).  Celko also calls this the Massively Unified Code Key. 

It's no coincidence that the acronym is MUCK! :-)

Storing data in this way destroys many of the advantages of relational databases such as DRI (Declarative Referential Integrity), CHECK constraints and DEFAULT values.

Please create a table with 100 fields and 10 rows - if that's what your data requires, then do it. Perhaps a couple of other fields with experiment ID, datetime and experimenter_id would also be useful? That way you can perform analyses over given periods, various other aggregates - basically slice and dice all of your data.

&lt; Personal opinion > If you haven't chosen your database yet and are happy to use F/LOSS, then may I recommend PostgreSQL - it's SQL dialect is by far the richest of the Open Source databases (I have no connection to the project). Check here for how to enforce datatypes in SQLite, but PostgreSQL offers more than SQLite - it's multi-user for example and no need to jump through hoops to enforce datatypes.&lt; / Personal opinion >

[EDIT1]

Just one further remark, and for completeness, there is only one significant system out there that makes use of the EAV model - and that's Magento (1, 2). Its principal niche is the fashion industry where the EAV model may be suitable for sparse tables (fashion items tend to be available in a myriad of colours, syles, sizes...). It is popular (1, 2), but then so is MySQL which is inferior in many ways to PostgreSQL, Firebird and (multi-user capability aside) SQLite.