Disadvantages Of Laptops:

Standardization issues
While there are accepted world standards of form factors for all the peripherals and add-in PC cards used in the desktop computers, there are still no firm worldwide standards relating to today's laptops' form factors internally, such as supply of electric voltage, motherboard layouts, internal adapters used in connecting the hard disk, optical drive, LCD cable, keyboard and floppy drive to the main board. Most affected by this are uneducated users, especially if they attempt to connect their laptops with incompatible hardware or power adapters.
Laptops are more complex than simple-to-use consumer electronics. A large number of different parts with similar functions may cause some difficulties to repair technicians, as they have to familiarize themselves with different sets of hardware, but this is part of the job in a specialized trade.

Compatibility issues
Any current compatibility problems in the laptop trade are reflective of the early era of personal computers, when there were many different manufacturers, each and every one of them having their own systems and incompatibility was more a norm.
Some mostly internal or proprietary parts made by laptop producers aren't interchangeable with other manufacturers' products, so that the same manufacturer's components are used with the laptop they produced. Some of the reasons for this are to ensure product stability, prolong product lifetime, to avoid dubious warranty issues and to protect computer beginners from harming their machines.
A significant point to note is that the vast majority of laptops on the market are manufactured by a small handful of ODMs. The ODM matters more than the OEM. Major relationships include:
Quanta sells to (among others) HP/Compaq, Dell, Toshiba, Sony, Fujitsu, Acer, NEC, Gateway and IBM - note that Quanta is currently (as of August, 2007) the largest manufacturer of notebook computers in the world
Compal sells to Toshiba, HP/Compaq, Acer, and Dell
Wistron sells to HP/Compaq, Dell, IBM, NEC, and Acer
Arima sells to HP/Compaq, NEC, and Dell
Uniwill/ECS sells to IBM, Fujitsu, and Dell
Asus sells to Apple (iBook), Sony, and Samsung
Inventec sells to HP/Compaq, Toshiba, and BenQ
To compensate, some manufacturers have and have had product lines where they have refrained from including some internal hardware in their products by adding in the number of standard hardware outlets and ports, thereby letting users choose their own hardware that they can connect.
In terms of hardware components standardization, PCMCIA/CardBus has proved to be a rather enduring standard. Older laptops lacking a USB port can have a PCMCIA USB/FireWire adapter plugged in. Modern adapters have two to four USB ports or they can be USB/Firewire combo adapters. Thus, such compatibility problems with getting hardware and peripherals connected has nowadays become a non-issue.

Free software
In some situations, users may have to pay for the additional cost that is wielded by some laptop manufacturers, by using their proprietary hardware extensions and including internal hardware that lacks documentation that would be instrumental in developing free software drivers.
Users of free and open-source software (FOSS) are more affected by this, as internal laptop hardware is not as easy or downright impossible to replace (when hardwired) than with stock desktop PC's. If internal laptop hardware is lacking drivers, it is of little use for free software operating systems (such as Linux and *BSD), and is essentially deadweight. To avoid such hardware, one must carefully research the desired products and choose manufacturers that are known for making good drivers or favoring free and open source software.

Naming conventions
Naming of features and parts used and/or their categories also differs from manufacturer to manufacturer, such as "system board" used by IBM and "motherboard" used by Compaq, "display cable", "LCD cable", "flexi-cable" are the terms used by the general public refer to the cable connecting the external display to the main board for transferring the digital signal (actual signalling is more or less standardized, though). Hardware problems with cables can be solved by correctly buying the right cables in the first place. Having some cable adapters is handy when dealing with hardware that was manufactured in different time periods by different standards.
The palm rest is called "palm rest" by Dell, the "keyboard bezel" by IBM and the "upper CPU cover" by Compaq and HP.
Similarly, some manufacturers prefer the term "Battery Life," while others use "Battery Run Time," to describe how long a laptop battery is able to supply operating power to the Laptop when disconnected from main power supply.

Upgradeability
Laptops' upgradeability is severely limited, both for technical and economic reasons. As of 2006, there is no industry-wide standard form factor for laptops. Each major laptop vendor pursues its own proprietary design and construction, with the result that laptops are difficult to upgrade and exhibit high repair costs. With few exceptions, laptop components can rarely be swapped between laptops of competing manufacturers, or even between laptops from the different product-lines of the same manufacturer. Standard feature peripherals (such as audio, video, USB, 1394, WiFi, Bluetooth) are generally integrated on the main PCB (motherboard), and thus upgrades often require using external ports, card slots, or wireless peripherals. Other components, such as RAM modules, hard drives, and batteries are typically user-upgradeable.
Many laptops have removable CPUs, although support for other CPUs is restricted to the specific models supported by the laptop motherboard. The socketed CPUs are perhaps for the manufacturer's convenience, rather than the end-user, as few manufacturers try new CPUs in last year's laptop model with an eye toward selling upgrades rather than new laptops. In many other laptops, the CPU is soldered and non-replaceable. Many laptops also include an internal MiniPCI slot, often occupied by a WiFi or Bluetooth card, but as with the CPU, the internal slot is often restricted in the range of cards that can be installed. The widespread adoption of USB mitigates I/O connectivity to a great degree, although the user must carry the USB peripheral as a separate item.
NVidia and ATI have proposed a standardized interface for laptop GPU upgrades (such as an MXM), but again, choices are limited compared to the desktop PCIe/AGP after-market.
On January 2007, Asus announced XG Station external video card for laptops. XG Station is connected to the laptops using USB-2 and Express card interface.
On February 2007, there is a new standard for external PCI Express cable and connector. Future laptops can be expanded using external PCI Express backplane and chassis.

Performance

A modern mid-range HP Laptop. It is best used as a desktop replacement
For a given price range (and manufacturing base), laptop computational power has traditionally trailed that of desktops. This is partly due to most laptops sharing RAM between the program memory and the graphics adapter. By virtue of their usage goals, laptops prioritize energy efficiency and compactness over absolute performance. Desktop computers and their modular components are built to fit much bigger standard enclosures, along with the expectation of AC line power. As such, energy efficiency and portability for desktops are secondary design goals compared to absolute performance.
For typical home (personal use) applications, where the computer spends the majority of its time sitting idle for the next user input, laptops of the thin-client type or larger are generally fast enough to achieve the required performance. 3D gaming, multimedia (video) encoding and playback, and analysis-packages (database, math, engineering, financial, etc.) are areas where desktops still offer the casual user a compelling advantage.
With the advent of dual-core processors and perpendicular recording, laptops are beginning to close the performance gap with PCs. Intel's Core 2 line of processors is efficient enough to be used in portable computers, and many manufacturers such as Apple and Dell are building Core 2 based laptops. Also, many high end laptop computers feature mobility versions of graphics cards, eliminating the performance losses associated with integrated graphics.

Health issues

Laptop coaster preventing heating of lap and improving laptop airflow.
A study by State University of New York researchers says heat generated from laptops can significantly elevate the temperature of the scrotum, potentially putting sperm count at risk. The study, which included more than two dozen men ages 13 to 35, found that the sitting position required to balance a laptop can raise scrotum temperature by as much as 2.1°C. Heat from the laptop itself can raise the temperature by another 0.7°C, bringing the potential total increase to 2.8°C. However, further research is needed to determine whether this directly affects sterility in men. A common practical solution to this problem is to place the laptop on a table or desk.

Security
Laptops are generally prized targets of theft, and theft of laptops can lead to more serious problems such as identity theft from stolen credit card numbers. Most laptops have a Kensington security slot to chain the computer to a desk with a third party security cable. In addition to this, modern operating systems and software may have disk encryption functionality that renders the data on the laptop's hard drive unreadable without a key, providing the laptop was not turned on while stolen.